CAT p.Ile109=
c.327C>T · rs61752922 · VCV782213
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.32%, 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 -2.3 | GERP -3.4 |
| Overall | ||
| CADD | 8.986 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.32%
European (non-Finnish) · 3,768/1,176,540 alleles
Filtering AF
0.312%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.308%
Overall
0.259%
4,170/1,610,374 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.32% | 312 |
| Remaining individualsnot grpmax-eligible | 0.232% | 430 |
| Admixed American | 0.173% | 577 |
| South Asian | 0.0824% | 1,214 |
| Finnishnot grpmax-eligible | 0.075% | 1,334 |
| Middle Eastern | 0.0496% | 2,018 |
| African / African-American | 0.0333% | 2,999 |
| East Asian | 0.00446% | 22,439 |
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
- CAT
- Protein
- p.Ile109=
- Coding
- c.327C>T
- MANE Select
- NM_001752
- dbSNP
- rs61752922
- Type
- single nucleotide variant
- Location
- chr11:34451076 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.97 · 17 PDB
- Residue 109
- a β-strand
Similar variants
- CAT c.239-5G>A Benign/Likely benign ★★ same type
- CAT p.Arg189Cys Benign/Likely benign ★★ same type
- CAT p.Asn439= Likely benign ★★ same type
- CAT p.Gly390Asp Benign ★★ same type
- CAT p.His209Tyr Likely benign ★★ same type
- CAT p.His492= Benign/Likely benign ★★ same type
- CAT p.Phe185= Benign/Likely benign ★★ same type
- CAT c.1057-2A>G 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/cat-p-ile109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown