CHN1 p.Leu401=
c.1203A>G · rs376483955 · VCV746053
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00769%, 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 -8.5 | GERP -3.6 |
| Overall | ||
| CADD | 0.718 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
South Asian · 7/91,010 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.00273%
44/1,612,454 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00769% | 13,001 |
| Admixed American | 0.00334% | 29,984 |
| European (non-Finnish) | 0.00288% | 34,670 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,384 |
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.Leu401=
- Coding
- c.1203A>G
- MANE Select
- NM_001822
- dbSNP
- rs376483955
- Type
- single nucleotide variant
- Location
- chr2:174801712 (GRCh38)
- Gene constraint
- LOEUF 0.79 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.41 · 2 PDB
- Residue 401
- the rho-gap domain; an α-helix
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-leu401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown