CNGA1 p.Val372=
c.1116C>G · rs1336098993 · VCV1148685
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, 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 1.9 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 5.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,992 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000434%
7/1,613,992 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,997 |
| African / African-American | 0.00133% | 74,920 |
| European (non-Finnish) | 0.000254% | 393,345 |
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
- CNGA1
- Protein
- p.Val372=
- Coding
- c.1116C>G
- MANE Select
- NM_001379270
- dbSNP
- rs1336098993
- Type
- single nucleotide variant
- Location
- chr4:47937366 (GRCh38)
- Gene constraint
- LOEUF 0.779 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.88 · 19 PDB
- Residue 372
- the 'ion conduction pathway' region; an α-helix
Similar variants
- CNGA1 c.107+1G>A Likely pathogenic ★★ same type
- CNGA1 c.107+2T>G Likely pathogenic ★★ same type
- CNGA1 c.545+2T>A Likely pathogenic ★★ same type
- CNGA1 c.545+2T>C Likely pathogenic ★★ same type
- CNGA1 c.546-1G>C Pathogenic/Likely pathogenic ★★ same type
- CNGA1 p.Arg214Ter Pathogenic ★★ same type
- CNGA1 p.Arg28Ter Pathogenic ★★ same type
- CNGA1 p.Arg420Ter 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/cnga1-p-val372 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown