CLCA4 p.Leu299=
c.895T>C · rs79822589 · VCV737467
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.27%, eas)
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 -6.3 | GERP -1.9 |
| Overall | ||
| CADD | 3.166 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.27%
East Asian · 571/44,852 alleles
Filtering AF
1.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.15%
Overall
0.0368%
594/1,613,354 alleles · low-frequency
exomes 559/1,461,226 · genomes 35/152,128 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.27% | 79 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,124 |
| Admixed American | 0.00333% | 29,985 |
| European (non-Finnish) | 8.48e-05% | 1,179,430 |
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
- CLCA4
- Protein
- p.Leu299=
- Coding
- c.895T>C
- MANE Select
- NM_012128
- dbSNP
- rs79822589
- Type
- single nucleotide variant
- Location
- chr1:86565961 (GRCh38)
- Gene constraint
- LOEUF 1.078 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.48
Similar variants
- CLCA4 p.Asp510Gly Uncertain significance ★★ ⚠ same type
- CLCA4 p.Gln485Ter Uncertain significance ★★ same type
- CLCA4 p.Arg113= Benign/Likely benign ★★ same type
- CLCA4 p.Ala235Thr Uncertain significance ★ ⚠ same type
- CLCA4 p.Ala353Val Uncertain significance ★ same type
- CLCA4 p.Ala431Thr Uncertain significance ★ ⚠ same type
- CLCA4 p.Ala431Val Uncertain significance ★ ⚠ same type
- CLCA4 p.Ala437Gly 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/clca4-p-leu299 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown