CAT p.Asp498=
c.1494C>T · VCV3358173
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0283%, amr)
Conditions
1
CAT-related disorder
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 0.41 | GERP 0.68, phastCons 0.99 |
| Overall | ||
| CADD | 5.831 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0283%
Admixed American · 17/60,004 alleles
Filtering AF
0.018%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.00112%
18/1,614,034 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0283% | 3,530 |
| European (non-Finnish) | 8.47e-05% | 1,179,993 |
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.Asp498=
- Coding
- c.1494C>T
- MANE Select
- NM_001752
- Type
- single nucleotide variant
- Location
- chr11:34471017 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.97 · 17 PDB
- Residue 498
- an α-helix
Disease context
CAT-related disorder
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-asp498 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown