CHMP6 p.Arg43=
c.129C>T · VCV4002458
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00687%, eas)
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 -2.9 | GERP -3.7 |
| Overall | ||
| CADD | 3.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00687%
East Asian · 3/43,680 alleles
Filtering AF
0.00198%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0017%
Overall
0.00252%
40/1,584,628 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00687% | 14,560 |
| European (non-Finnish) | 0.00274% | 36,492 |
| South Asian | 0.00231% | 43,269 |
| Admixed American | 0.00183% | 54,678 |
| Finnishnot grpmax-eligible | 0.00166% | 60,178 |
| African / African-American | 0.00134% | 74,464 |
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
- CHMP6
- Protein
- p.Arg43=
- Coding
- c.129C>T
- MANE Select
- NM_024591
- Type
- single nucleotide variant
- Location
- chr17:80994646 (GRCh38)
- Gene constraint
- LOEUF 0.599 · pLI 0.76 (gnomAD)
- Structure
- AlphaFold pLDDT 82.51 · 2 PDB
- Residue 43
- an α-helix
Similar variants
- CHMP6 p.Asn185= Benign ★★ same type
- CHMP6 p.Gly55Ser Benign ★★ same type
- CHMP6 p.Ala190Asp Uncertain significance ★ ⚠ same type
- CHMP6 p.Ala46Thr Uncertain significance ★ ⚠ same type
- CHMP6 p.Arg12Pro Uncertain significance ★ ⚠ same type
- CHMP6 p.Arg138Gln Uncertain significance ★ ⚠ same type
- CHMP6 p.Arg45Cys Uncertain significance ★ same type
- CHMP6 p.Arg45His 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/chmp6-p-arg43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown