VMA22 p.Ser61=
c.183C>T · VCV4788795
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0148%, afr)
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 0.45 | phastCons 0.49 |
| Overall | ||
| CADD | 11.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0148%
African / African-American · 11/74,464 alleles
Filtering AF
0.0082%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00637%
Overall
0.000744%
12/1,612,074 alleles · ultra-rare
exomes 4/1,461,206 · genomes 8/150,868 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0148% | 6,769 |
| Admixed American | 0.00167% | 59,724 |
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
- VMA22
- Protein
- p.Ser61=
- Coding
- c.183C>T
- MANE Select
- NM_032357
- Type
- single nucleotide variant
- Location
- chr2:130341873 (GRCh38)
- Structure
- AlphaFold pLDDT 83.32
Similar variants
- VMA22 p.Leu31Ser Pathogenic ★★ same type
- VMA22 p.Arg102Gln Uncertain significance ★★ ⚠ same type
- VMA22 p.Leu147Pro Uncertain significance ★★ ⚠ same type
- VMA22 p.Met49Lys Uncertain significance ★★ ⚠ same type
- VMA22 p.Ser72Arg Uncertain significance ★★ ⚠ same type
- VMA22 c.-402C>T Benign ★★ same type
- VMA22 p.Ala148= Benign/Likely benign ★★ same type
- VMA22 p.Ala180Val Likely benign ★★ 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/vma22-p-ser61 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown