CHRNG p.Pro420=
c.1260G>A · rs376569365 · VCV2988290
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.115%, amr)
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 -6 | GERP -3.1 |
| Overall | ||
| CADD | 0.175 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.115%
Admixed American · 69/60,004 alleles
Filtering AF
0.0932%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0852%
Overall
0.00706%
114/1,613,868 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.115% | 870 |
| South Asian | 0.0154% | 6,506 |
| East Asian | 0.00668% | 14,960 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,621 |
| African / African-American | 0.00267% | 37,450 |
| European (non-Finnish) | 0.00186% | 53,637 |
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
- CHRNG
- Protein
- p.Pro420=
- Coding
- c.1260G>A
- MANE Select
- NM_005199
- dbSNP
- rs376569365
- Type
- single nucleotide variant
- Location
- chr2:232544782 (GRCh38)
- Gene constraint
- LOEUF 1.286 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.91
Similar variants
- CHRNG p.Pro420Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- CHRNG c.1380+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHRNG c.350+2T>C Pathogenic/Likely pathogenic ★★ same type
- CHRNG c.351-2A>G Likely pathogenic ★★ same type
- CHRNG c.56-1G>A Pathogenic ★★ same type
- CHRNG c.805+1G>A Likely pathogenic ★★ same type
- CHRNG p.Arg239Cys Pathogenic ★★ same type
- CHRNG p.Arg341Ter Pathogenic/Likely pathogenic ★★ 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/chrng-p-pro420 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown