Summary: Cleft lip and palate transmembrane protein 1 (CLPTM1)

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Wikipedia: Cleft lip and palate transmembrane protein 1
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This is the Wikipedia entry entitled "Cleft lip and palate transmembrane protein 1". More...

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Cleft lip and palate transmembrane protein 1 Edit Wikipedia article

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CLPTM1

Identifiers

Aliases

CLPTM1, transmembrane protein, CLPTM1 regulator of GABA type A receptor forward trafficking

External IDs

OMIM: 604783 MGI: 1927155 HomoloGene: 37464 GeneCards: CLPTM1

Gene location (Human)

Chr.	Chromosome 19 (human)^[1]

Band	19q13.32	Start	44,954,585 bp^[1]
Band	19q13.32	End	44,993,341 bp^[1]

Gene location (Mouse)

Chr.	Chromosome 7 (mouse)^[2]

Band	7\|7 A3	Start	19,365,496 bp^[2]
Band	7\|7 A3	End	19,398,958 bp^[2]

RNA expression pattern

Bgee

Top expressed in
putamen caudate nucleus hypothalamus
More reference expression data

BioGPS


More reference expression data

Gene ontology
Molecular function	GO:0001948 protein binding
Cellular component	integral component of membrane integral component of plasma membrane membrane external side of plasma membrane
Biological process	multicellular organism development regulation of T cell differentiation in thymus cell differentiation
Sources:Amigo / QuickGO

Orthologs

Species

Human

Mouse

Entrez


1209


56457

Ensembl


ENSG00000104853


ENSMUSG00000002981

UniProt


O96005


Q8VBZ3

RefSeq (mRNA)


NM_001294 NM_001199468 NM_001282175 NM_001282176


NM_019649

RefSeq (protein)


NP_001269104 NP_001269105 NP_001285


NP_062623

Location (UCSC)

Chr 19: 44.95 â€“ 44.99 Mb

Chr 7: 19.37 â€“ 19.4 Mb

PubMed search

^[3]

^[4]

Wikidata

View/Edit Human

View/Edit Mouse

Cleft lip and palate associated transmembrane protein 1, also known as CLPTM1, is a human gene.^[5]

Template:PBB Summary

References

^ ^a ^b ^c GRCh38: Ensembl release 89: ENSG00000104853 - Ensembl, May 2017
^ ^a ^b ^c GRCm38: Ensembl release 89: ENSMUSG00000002981 - Ensembl, May 2017
^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
^ "Entrez Gene: CLPTM1 cleft lip and palate associated transmembrane protein 1".

Cleft lip and palate transmembrane protein 1 (CLPTM1) Provide feedback

This family consists of several eukaryotic cleft lip and palate transmembrane protein 1 sequences. Cleft lip with or without cleft palate is a common birth defect that is genetically complex. The nonsyndromic forms have been studied genetically using linkage and candidate-gene association studies with only partial success in defining the loci responsible for orofacial clefting. CLPTM1 encodes a transmembrane protein and has strong homology to two Caenorhabditis elegans genes, suggesting that CLPTM1 may belong to a new gene family [1]. This family also contains the human cisplatin resistance related protein CRR9p which is associated with CDDP-induced apoptosis [2].

Literature references

Yoshiura K, Machida J, Daack-Hirsch S, Patil SR, Ashworth LK, Hecht JT, Murray JC; , Genomics 1998;54:231-240.: Characterization of a novel gene disrupted by a balanced chromosomal translocation t(2;19)(q11.2;q13.3) in a family with cleft lip and palate. PUBMED:9828125 EPMC:9828125
Yamamoto K, Okamoto A, Isonishi S, Ochiai K, Ohtake Y; , Biochem Biophys Res Commun 2001;280:1148-1154.: A novel gene, CRR9, which was up-regulated in CDDP-resistant ovarian tumor cell line, was associated with apoptosis. PUBMED:11162647 EPMC:11162647

This tab holds annotation information from the InterPro database.

InterPro entry IPR008429

This entry includes cleft lip and palate transmembrane protein 1 (CLPTM1) and cleft lip and palate transmembrane protein 1-like protein (CLPTM1L, also known as CRR9). This entry also includes uncharacterised proteins from fungi and plants.

Clefts of the lip and/or palate (CL/P) are some of the most common birth defects. They may be categorised into syndromic or non-syndromic types, with syndromic defects having an underlying chromosomal or teratogenic cause. Around 70% of clefts are non-syndromic and individuals have no typical physical or developmental abnormalities; these clefts generally show polygenetic behaviour and complex inheritance [ PUBMED:16122939 ]. Studies have identified regions on chromosomes 19 and 11 which may be involved in non-syndromic cleft lip and palates; this included a novel gene on chromosome 19, cleft lip and palate-associated transmembrane protein 1 (CLPTM1) [ PUBMED:9828125 ]. The Poliovirus receptor-related 1 gene (PVRL1), which is located on chromosome 11, has also been shown to associate with non-syndromic cleft lip and palates [ PUBMED:11559849 , PUBMED:19715471 ].

Human CLPTM1L protects non-small cell lung cancer tumour cells from genotoxic apoptosis and may contribute to lung cancer risk [ PUBMED:24366883 , PUBMED:22675468 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component

integral component of membrane (GO:0016021)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (124)	Full (2940)	Representative proteomes				UniProt (5103)
	Seed (124)	Full (2940)	RP15 (629)	RP35 (1272)	RP55 (2265)	RP75 (3021)	UniProt (5103)
Jalview	View	View	View	View	View	View	View
HTML	View	View
PP/heatmap	₁	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (124)	Full (2940)	Representative proteomes				UniProt (5103)
	Seed (124)	Full (2940)	RP15 (629)	RP35 (1272)	RP55 (2265)	RP75 (3021)	UniProt (5103)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (124)	Full (2940)	Representative proteomes				UniProt (5103)
	Seed (124)	Full (2940)	RP15 (629)	RP35 (1272)	RP55 (2265)	RP75 (3021)	UniProt (5103)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Pfam-B_8636 (release 8.0)

Previous IDs:

none

Type:

Family

Sequence Ontology:

SO:0100021

Author:

Moxon SJ

Number in seed:

124

Number in full:

2940

Average length of the domain:

372.5 aa

Average identity of full alignment:

31 %

Average coverage of the sequence by the domain:

70.7 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	22.0	22.0
Trusted cut-off	22.1	22.0
Noise cut-off	21.8	21.8

Model length:

435

Family (HMM) version:

15

Download:

download the raw HMM for this family

Species distribution

Sunburst
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Colour assignments

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Selections

Align selected sequences to HMM

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein	Predicted structure	External Information
A0A044TRQ1	View 3D Structure	Click here
A0A077ZH95	View 3D Structure	Click here
A0A077ZJY0	View 3D Structure	Click here
A0A077ZL17	View 3D Structure	Click here
A0A0D2DEJ7	View 3D Structure	Click here
A0A0K0E8G7	View 3D Structure	Click here
A0A0K0EJ55	View 3D Structure	Click here
A0A0N4U9E9	View 3D Structure	Click here
A0A0N4ULL1	View 3D Structure	Click here
A0A175W4D8	View 3D Structure	Click here
A0A1C1CPT7	View 3D Structure	Click here
A0A1D6E9Z1	View 3D Structure	Click here
A0A1D6IZI4	View 3D Structure	Click here
A0A1X7YHG5	View 3D Structure	Click here
A0A2K6VG65	View 3D Structure	Click here
A0A3P7E0W6	View 3D Structure	Click here
A0A3Q0KP13	View 3D Structure	Click here
A0A3Q0KUL3	View 3D Structure	Click here
A0A5S6PR23	View 3D Structure	Click here
A0A7I4KCK5	View 3D Structure	Click here
A2VE61	View 3D Structure	Click here
A4I9H3	View 3D Structure	Click here
B2RYF6	View 3D Structure	Click here
C0NHJ0	View 3D Structure	Click here
C1H1G4	View 3D Structure	Click here
D4A416	View 3D Structure	Click here
I1JXT8	View 3D Structure	Click here
I1KBT9	View 3D Structure	Click here
O96005	View 3D Structure	Click here
Q22003	View 3D Structure	Click here
Q2NL17	View 3D Structure	Click here
Q38BZ8	View 3D Structure	Click here
Q4CRX9	View 3D Structure	Click here
Q4D2P5	View 3D Structure	Click here
Q54RJ1	View 3D Structure	Click here
Q5R7B1	View 3D Structure	Click here
Q5ZKJ0	View 3D Structure	Click here
Q6DEL2	View 3D Structure	Click here
Q6DHU1	View 3D Structure	Click here
Q7FA04	View 3D Structure	Click here

Showing 40 matches

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trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;

Family: CLPTM1 (PF05602)

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