CLTRN
protein-codingcollectrin, amino acid transport regulator
Gene summary
This gene encodes a type 1 transmembrane protein that is important for trafficking amino acid transporters to the apical brush border of proximal tubules. The encoded protein binds to amino acid transporters and regulates their expression on the plasma membrane. It also plays a role in controlling insulin exocytosis by regulating formation of the SNARE (soluble N-ethylmaleimide-sensitive-factor attachment protein receptor) complex in pancreatic beta cells. The extracellular domain of the encoded protein may be cleaved and shed from the plasma membrane specifically in pancreatic beta cells. [provided by RefSeq, Jun 2013]
- TMEM27
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~47.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009324
Submitter: Orphanet
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CLTRN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020665.6. 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 | 5 | 5 | ||||
| missense | 36 | 2 | 38 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 46 | 2 | 0 | 48 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065716.1 | 6 | MANE Select | |
| Ensembl | ENSP00000369699.3 | 6 | MANE Select | |
| Ensembl | ENSP00000497814.1 | 4 | Standard | |
| Ensembl | ENSP00000497814.1 | 4 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000380342
- Coding exons
- 6
- Length
- 37714
- Individuals with no LoFs
- 125678
- Homozygous LoFs
- 9
- Heterozygous LoFs
- 32
- Defined
- 125719
- p
- 0.000163
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.279 | 81 | 74.2 | 1.09 | 0.00000513 | 1465 |
| Missense (PolyPhen) | 25 | 19.647 | 1.2725 | 432 | ||
| Synonymous | 0.824 | 20 | 25.3 | 0.791 | 0.00000173 | 417 |
| Loss of Function | 0.0861 | 6 | 6.23 | 0.963 | 3.93e-7 | 126 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.0010 | 0.00081 | notable |
| Ashkenazi Jewish | 0.00014 | 0.000099 | rare |
| East Asian | 0.000075 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000075 | 0.000053 | rare |
| South Asian | 0.00011 | 0.000065 | rare |
| Other | 0.00067 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulator of SNARE complex function. Stimulator of beta cell replication. {ECO:0000269|PubMed:16330323}.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- RVIS EVS
- -0.19
- RVIS percentile EVS
- 39.68
Essentials
- Essential (gene trap)
- N