Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 1420  species 0  interactions 2940  sequences 43  architectures

Family: CLPTM1 (PF05602)

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

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Cleft lip and palate transmembrane protein 1 Edit Wikipedia article

Template:PBB Controls

CLPTM1
Identifiers
AliasesCLPTM1, transmembrane protein, CLPTM1 regulator of GABA type A receptor forward trafficking
External IDsOMIM: 604783 MGI: 1927155 HomoloGene: 37464 GeneCards: CLPTM1
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
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 – 44.99 MbChr 7: 19.37 – 19.4 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

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

Template:PBB Summary

References

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

Further reading

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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

  1. 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

  2. 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.

Domain organisation

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

Loading domain graphics...

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...

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)
RP15
(629)
RP35
(1272)
RP55
(2265)
RP75
(3021)
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, x not generated, not available.

Format an alignment

  Seed
(124)
Full
(2940)
Representative proteomes UniProt
(5103)
RP15
(629)
RP35
(1272)
RP55
(2265)
RP75
(3021)
Alignment:
Format:
Order:
Sequence:
Gaps:
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)
RP15
(629)
RP35
(1272)
RP55
(2265)
RP75
(3021)
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 View help on the curation process

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 View help on HMM parameters

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 controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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

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;