CHN1 p.Asp433=
c.1299C>T · rs1326246983 · VCV722706
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00275%, sas)
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 -3.9 | GERP -3.9 |
| Overall | ||
| CADD | 4.587 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00275%
South Asian · 2/72,804 alleles
Filtering AF
0.000517%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000378%
Overall
0.000983%
15/1,526,022 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00275% | 36,402 |
| Finnishnot grpmax-eligible | 0.00165% | 60,472 |
| African / African-American | 0.00139% | 71,910 |
| European (non-Finnish) | 0.000963% | 103,789 |
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
- CHN1
- Protein
- p.Asp433=
- Coding
- c.1299C>T
- MANE Select
- NM_001822
- dbSNP
- rs1326246983
- Type
- single nucleotide variant
- Location
- chr2:174800197 (GRCh38)
- Gene constraint
- LOEUF 0.79 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.41 · 2 PDB
- Residue 433
- the rho-gap domain
Similar variants
- CHN1 c.-160C>G Uncertain significance ★★ same type
- CHN1 c.-74C>T Uncertain significance ★★ same type
- CHN1 p.Ala27Gly Uncertain significance ★★ ⚠ same type
- CHN1 p.Asp440Gly Uncertain significance ★★ ⚠ same type
- CHN1 p.Lys260Asn Uncertain significance ★★ ⚠ same type
- CHN1 p.Thr167Ile Uncertain significance ★★ ⚠ same type
- CHN1 p.Val65Met Uncertain significance ★★ ⚠ same type
- CHN1 c.886+15G>A 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/chn1-p-asp433 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown