CHMP1A p.Pro142=
c.426G>A · rs370480409 · VCV2955992
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.076 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -3.4 |
| Overall | ||
| CADD | 2.774 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,080 alleles
Filtering AF
0.00517%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00388%
Overall
0.00342%
55/1,610,490 alleles · ultra-rare
exomes 50/1,458,278 · genomes 5/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,080 |
| South Asian | 0.00996% | 10,038 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,592 |
| European (non-Finnish) | 0.00339% | 29,475 |
| Finnishnot grpmax-eligible | 0.00159% | 62,896 |
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.Pro142=
- Coding
- c.426G>A
- MANE Select
- NM_002768
- dbSNP
- rs370480409
- Type
- single nucleotide variant
- Location
- chr16:89646670 (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 condition
- CHMP1A p.Arg46Cys Uncertain significance ★★ ⚠ same condition
- CHMP1A p.Arg54Cys Uncertain significance ★★ ⚠ same condition
- CHMP1A p.Arg64Trp Uncertain significance ★★ ⚠ same condition
- CHMP1A p.Gly59Ser Uncertain significance ★★ ⚠ same condition
- CHMP1A p.Lys27Asn Uncertain significance ★★ same condition
- CHMP1A p.Ser127Trp Uncertain significance ★★ ⚠ same condition
- CHMP1A p.Ser135= Uncertain significance ★★ same condition
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-pro142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown