CHMP1A p.Pro169=
c.507C>T · rs61730918 · VCV384618
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.47%, 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 -7.6 | GERP -3.4 |
| Overall | ||
| CADD | 2.914 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.47%
African / African-American · 1,100/74,828 alleles
Filtering AF
1.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.37%
Overall
0.0759%
1,214/1,600,002 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.47% | 68 |
| Remaining individualsnot grpmax-eligible | 0.071% | 1,408 |
| Admixed American | 0.0673% | 1,485 |
| Middle Eastern | 0.0166% | 6,040 |
| South Asian | 0.0159% | 6,307 |
| European (non-Finnish) | 0.00136% | 73,416 |
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.Pro169=
- Coding
- c.507C>T
- MANE Select
- NM_002768
- dbSNP
- rs61730918
- Type
- single nucleotide variant
- Location
- chr16:89646589 (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 c.28-13G>A Pathogenic/Likely pathogenic ★★ same type
- CHMP1A p.Ala172Thr Uncertain significance ★★ ⚠ 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-pro169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown