AGAP6 p.Val49=
c.147A>G · rs371327390 · VCV2640466
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.145%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.72 | phastCons 0.026 |
| Overall | ||
| CADD | 2.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.145%
South Asian · 132/90,806 alleles
Filtering AF
0.125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.118%
Overall
0.026%
414/1,593,090 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.145% | 688 |
| East Asian | 0.0492% | 2,033 |
| Middle Eastern | 0.0381% | 2,625 |
| Remaining individualsnot grpmax-eligible | 0.0241% | 4,144 |
| European (non-Finnish) | 0.0187% | 5,342 |
| Finnishnot grpmax-eligible | 0.0158% | 6,342 |
| Admixed American | 0.0117% | 8,523 |
| African / African-American | 0.0108% | 9,254 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- AGAP6
- Protein
- p.Val49=
- Coding
- c.147A>G
- MANE Select
- NM_001077665
- dbSNP
- rs371327390
- Type
- single nucleotide variant
- Location
- chr10:49988862 (GRCh38)
- Gene constraint
- LOEUF 0.757 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.73
Similar variants
- AGAP6 p.Ala105Thr Uncertain significance ★ ⚠ same type
- AGAP6 p.Ala109Thr Uncertain significance ★ ⚠ same type
- AGAP6 p.Ala135Val Uncertain significance ★ ⚠ same type
- AGAP6 p.Ala180Gly Uncertain significance ★ ⚠ same type
- AGAP6 p.Ala425Thr Uncertain significance ★ ⚠ same type
- AGAP6 p.Ala433Val Uncertain significance ★ ⚠ same type
- AGAP6 p.Ala43Ser Uncertain significance ★ ⚠ same type
- AGAP6 p.Ala444Pro Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/agap6-p-val49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown