Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.06%, mid)
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 -0.13 | GERP 0.61 |
| Overall | ||
| CADD | 10.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.06%
Middle Eastern · 64/6,062 alleles
Filtering AF
0.848%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.773%
Overall
0.221%
3,567/1,614,032 alleles · low-frequency
exomes 3,310/1,461,688 · genomes 257/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.06% | 95 |
| Ashkenazi Jewishnot grpmax-eligible | 0.473% | 211 |
| European (non-Finnish) | 0.251% | 399 |
| Remaining individualsnot grpmax-eligible | 0.229% | 437 |
| Finnishnot grpmax-eligible | 0.111% | 902 |
| South Asian | 0.0988% | 1,012 |
| Admixed American | 0.0966% | 1,035 |
| African / African-American | 0.0533% | 1,876 |
| East Asian | 0.00223% | 44,868 |
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.Arg113=
- Coding
- c.339A>G
- MANE Select
- NM_012128
- dbSNP
- rs2231583
- Type
- single nucleotide variant
- Location
- chr1:86560249 (GRCh38)
- Gene constraint
- LOEUF 1.078 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.48
- Residue 113
- the 'metalloprotease domain' region
Similar variants
- CLCA4 p.Asp510Gly Uncertain significance ★★ ⚠ same type
- CLCA4 p.Gln485Ter Uncertain significance ★★ 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
- CLCA4 p.Ala437Val 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-arg113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown