CLMP
protein-codingCXADR like membrane protein, the group of IgCAM CXADR-related subfamily|I-set domain containing
Gene summary
This gene encodes a type I transmembrane protein that is localized to junctional complexes between endothelial and epithelial cells and may have a role in cell-cell adhesion. Expression of this gene in white adipose tissue is implicated in adipocyte maturation and development of obesity. This gene is also essential for normal intestinal development and mutations in the gene are associated with congenital short bowel syndrome. [provided by RefSeq, Aug 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~125.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0020718
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0020718
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014097
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0020718
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Gastrointestinal
Intervention: Gastrointestinal
Rationale: Individuals have been described as benefiting from early introduction of enteral feeds, with later weaning from parenteral nutrition; Awareness of the risk of other GI-related complications may allow prompt recognition and management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CLMP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024769.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 4 | 8 | |||
| missense | 2 | 49 | 2 | 53 | ||
| nonsense | 2 | 4 | 6 | |||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 2 | 3 | |||
| Total | 5 | 5 | 51 | 6 | 4 | 71 |
Highest pathogenic variant AF is 0.000012313317
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079045.1 | 7 | MANE Select | |
| Ensembl | ENSP00000405577.2 | 7 | MANE Select | |
| Ensembl | ENSP00000520511.1 | 7 | Standard | |
| Ensembl | ENSP00000520511.1 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| clmpa | Danio rerio | Structure: intestine Quality: decreased length abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- digestive tract development
Cellular Component
- cytoplasmic microtubule
- plasma membrane
- bicellular tight junction
- cell surface
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000448775
- Coding exons
- 7
- Length
- 122955
- Individuals with no LoFs
- 125722
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 26
- Defined
- 125748
- p
- 0.000103
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.583 | 183 | 207 | 0.886 | 0.0000112 | 2359 |
| Missense (PolyPhen) | 68 | 69.432 | 0.97937 | 825 | ||
| Synonymous | 0.216 | 76 | 78.4 | 0.969 | 0.00000390 | 782 |
| Loss of Function | 1.55 | 14 | 21.8 | 0.642 | 0.00000144 | 224 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000059 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00015 | 0.00015 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in the cell-cell adhesion. May play a role in adipocyte differentiation and development of obesity. Is required for normal small intestine development. {ECO:0000269|PubMed:14573622, ECO:0000269|PubMed:15563274, ECO:0000269|PubMed:22155368}.;
- Disease
- DISEASE: Congenital short bowel syndrome (CSBS) [MIM:615237]: A disease characterized by a shortened small intestine, intestinal malrotation, and malabsorption. The mean length of the small intestine in CSBS patients is approximately 50 cm, compared with a normal length at birth of 190-280 cm. Patients with CSBS may develop severe malnutrition as a result of the hugely reduced absorptive surface of the small intestine. Infants require parenteral nutrition for survival. However, parenteral nutrition itself causes life-threatening complications such as sepsis and liver failure which are associated with a high rate of mortality early in life. {ECO:0000269|PubMed:22155368}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 57.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |