CAT p.Ser417=
c.1251T>C · rs200089024 · VCV725235
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0433%, amr)
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 -12 | GERP -3.1 |
| Overall | ||
| CADD | 0.109 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0433%
Admixed American · 26/60,032 alleles
Filtering AF
0.0303%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.026%
Overall
0.0018%
29/1,614,172 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0433% | 2,309 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,253 |
| European (non-Finnish) | 8.47e-05% | 1,179,981 |
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.Ser417=
- Coding
- c.1251T>C
- MANE Select
- NM_001752
- dbSNP
- rs200089024
- Type
- single nucleotide variant
- Location
- chr11:34464160 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.97 · 17 PDB
- Residue 417
- a modified residue (phosphoserine); an α-helix
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.Ile109= Benign/Likely benign ★★ same type
- CAT p.Phe185= Benign/Likely benign ★★ 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-ser417 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown