CA6 p.Ile299=
c.897T>C · VCV3904821
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.01%, nfe)
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 -2.7 | GERP -2.9 |
| Overall | ||
| CADD | 0.138 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.01%
European (non-Finnish) · 11,886/1,174,372 alleles
Filtering AF
0.997%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.991%
Overall
0.8%
12,834/1,604,018 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.01% | 99 |
| Amishnot grpmax-eligible | 0.658% | 152 |
| Remaining individualsnot grpmax-eligible | 0.589% | 170 |
| Finnishnot grpmax-eligible | 0.421% | 238 |
| Ashkenazi Jewishnot grpmax-eligible | 0.191% | 525 |
| African / African-American | 0.146% | 685 |
| South Asian | 0.104% | 963 |
| Admixed American | 0.079% | 1,266 |
| Middle Eastern | 0.0497% | 2,013 |
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
- CA6
- Protein
- p.Ile299=
- Coding
- c.897T>C
- MANE Select
- NM_001215
- Type
- single nucleotide variant
- Location
- chr1:8974674 (GRCh38)
- Gene constraint
- LOEUF 1.218 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49 · 1 PDB
Similar variants
- CA6 p.Gly70= Benign ★★ same type
- CA6 p.Ala33Val Uncertain significance ★ ⚠ same type
- CA6 p.Arg255Cys Uncertain significance ★ ⚠ same type
- CA6 p.Arg255Ser Uncertain significance ★ ⚠ same type
- CA6 p.Arg265Gly Uncertain significance ★ ⚠ same type
- CA6 p.Arg305Gly Uncertain significance ★ ⚠ same type
- CA6 p.Arg96Gly Uncertain significance ★ ⚠ same type
- CA6 p.Asn280Tyr Uncertain significance ★ ⚠ 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/ca6-p-ile299 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown