HEPACAM2
protein-codingHEPACAM family member 2, the group of V-set domain containing|I-set domain containing
Gene summary
This gene encodes a protein related to the immunoglobulin superfamily that plays a role in mitosis. Knockdown of this gene results in prometaphase arrest, abnormal nuclear morphology and apoptosis. Poly(ADP-ribosylation) of the encoded protein promotes its translocation to centrosomes, which may stimulate centrosome maturation. A chromosomal deletion including this gene may be associated with myeloid leukemia and myelodysplastic syndrome in human patients. [provided by RefSeq, Oct 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~37.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0007661
Submitter: Labcorp Genetics (formerly Invitae)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HEPACAM2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001039372.4. 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 | 1 | 1 | ||||
| missense | 59 | 3 | 1 | 63 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 66 | 4 | 1 | 71 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001034461.1 | 10 | MANE Select | |
| Ensembl | ENSP00000377980.2 | 10 | MANE Select | |
| RefSeq | NP_001275733.1 | 11 | Standard | |
| RefSeq | NP_001275739.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- centrosome cycle
- cell division
Molecular Function
- protein binding
Cellular Component
- Golgi membrane
- Golgi apparatus
- centrosome
- spindle
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000394468
- Coding exons
- 10
- Length
- 37939
- Individuals with no LoFs
- 125603
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 133
- Defined
- 125737
- p
- 0.000533
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.252 | 237 | 248 | 0.955 | 0.0000118 | 3021 |
| Missense (PolyPhen) | 73 | 92.593 | 0.7884 | 1145 | ||
| Synonymous | 0.368 | 88 | 92.5 | 0.951 | 0.00000463 | 904 |
| Loss of Function | 0.688 | 17 | 20.3 | 0.835 | 8.59e-7 | 264 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00047 | 0.00046 | rare |
| Ashkenazi Jewish | 0.00040 | 0.00040 | rare |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00027 | 0.00026 | rare |
| South Asian | 0.0019 | 0.0018 | notable |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required during prometaphase for centrosome maturation. Following poly-ADP-ribosylation (PARsylation) by TNKS, translocates from the Golgi apparatus to mitotic centrosomes and plays a key role in the formation of robust microtubules for prompt movement of chromosomes: anchors AKAP9/CG-NAP, a scaffold protein of the gamma-tubulin ring complex and promotes centrosome maturation. {ECO:0000269|PubMed:22864114}.;
Recessive Scores
- pRec
- 0.0932
Intolerance Scores
- LoFtool
- 0.931
- RVIS EVS
- 0.64
- RVIS percentile EVS
- 83.9
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0838
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |