CHMP1A p.Ala172=
c.516C>T · rs1172323559 · VCV1940731
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000937%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.045 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.29 | GERP -3.4, phastCons 0.018 |
| Overall | ||
| CADD | 7.292 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000937%
European (non-Finnish) · 11/1,173,470 alleles
Filtering AF
0.000503%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000368%
Overall
0.000689%
11/1,597,488 alleles · very rare
exomes 10/1,445,260 · genomes 1/152,228 · joint denominator
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
- CHMP1A
- Protein
- p.Ala172=
- Coding
- c.516C>T
- MANE Select
- NM_002768
- dbSNP
- rs1172323559
- Type
- single nucleotide variant
- Location
- chr16:89646580 (GRCh38)
- Gene constraint
- LOEUF 1.045 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.44 · 4 PDB
Similar variants
- CHMP1A p.Ala172Thr Uncertain significance ★★ ⚠ same residue
- CHMP1A c.28-13G>A Pathogenic/Likely pathogenic ★★ same type
- CHMP1A p.Arg46Cys Uncertain significance ★★ ⚠ same type
- CHMP1A p.Arg54Cys Uncertain significance ★★ ⚠ same type
- CHMP1A p.Arg64Trp Uncertain significance ★★ ⚠ same type
- CHMP1A p.Cys44Ser Uncertain significance ★★ ⚠ same type
- CHMP1A p.Gln186His Uncertain significance ★★ ⚠ same type
- CHMP1A p.Gly59Ser 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/chmp1a-p-ala172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown