CA4 p.Asp161=
c.483C>T · rs550453527 · VCV1920008
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0198%, sas)
Conditions
1
inherited retinal dystrophy
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 -5.9 | GERP -3.3 |
| Overall | ||
| CADD | 1.701 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0198%
South Asian · 18/91,086 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00297%
48/1,613,828 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0198% | 5,060 |
| East Asian | 0.00891% | 11,220 |
| Admixed American | 0.00333% | 30,002 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| African / African-American | 0.00267% | 37,473 |
| European (non-Finnish) | 0.0017% | 58,990 |
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
- CA4
- Protein
- p.Asp161=
- Coding
- c.483C>T
- MANE Select
- NM_000717
- dbSNP
- rs550453527
- Type
- single nucleotide variant
- Location
- chr17:60157758 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.86 · 10 PDB
- Residue 161
- a disulfide bond; the alpha-carbonic anhydrase domain
Similar variants
- CA4 p.Asp268Asn Uncertain significance ★★ ⚠ same condition
- CA4 p.Ala164= Benign/Likely benign ★★ same condition
- CA4 p.Asn177Lys Benign/Likely benign ★★ same condition
- CA4 p.Lys145= Benign/Likely benign ★★ same condition
- CA4 p.Pro287= Benign/Likely benign ★★ same condition
- CA4 p.Ser119= Benign/Likely benign ★★ same condition
- CA4 p.Cys229Ter Likely pathogenic ★ same condition
- CA4 p.Ter313Arg Likely pathogenic ★ same condition
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/ca4-p-asp161 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown