GARIN1A
protein-codinggolgi associated RAB2 interactor 1A
Gene summary
Predicted to be involved in acrosome assembly. Predicted to be located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]
- FAM137B
- FAM71F2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GARIN1A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001128926.4. 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 | 2 | 2 | ||||
| missense | 49 | 5 | 54 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 52 | 5 | 0 | 57 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001122398.1 | 5 | MANE Select | |
| Ensembl | ENSP00000506740.1 | 5 | MANE Select | |
| RefSeq | NP_001012457.3 | 5 | Standard | |
| RefSeq | NP_001277183.1 | 4 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000480462
- Coding exons
- 5
- Length
- 14588
- Individuals with no LoFs
- 124503
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 135
- Defined
- 124638
- p
- 0.000542
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.168 | 165 | 159 | 1.04 | 0.00000823 | 1983 |
| Missense (PolyPhen) | 60 | 59.39 | 1.0103 | 728 | ||
| Synonymous | -0.590 | 74 | 67.8 | 1.09 | 0.00000399 | 621 |
| Loss of Function | 1.58 | 4 | 9.15 | 0.437 | 4.85e-7 | 105 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00020 | 0.00019 | rare |
| Latino/Admixed American | 0.000062 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.0026 | 0.0026 | notable |
| European (Non-Finnish) | 0.00065 | 0.00063 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00051 | 0.00050 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.781
- RVIS EVS
- 1.28
- RVIS percentile EVS
- 93.77
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0325
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |