Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 45.5%, eas) — too common for a highly-penetrant pathogenic allele
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 -9.3 | GERP -2.5 |
| Overall | ||
| CADD | 2.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
45.5%
East Asian · 20,391/44,858 alleles
Filtering AF
44.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 44.7%
Overall
23.1%
373,285/1,613,666 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 45.5% | 2 |
| Amishnot grpmax-eligible | 35.7% | 3 |
| Middle Eastern | 31.1% | 3 |
| Admixed American | 29.8% | 3 |
| Remaining individualsnot grpmax-eligible | 25.1% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 24.3% | 4 |
| South Asian | 23.7% | 4 |
| European (non-Finnish) | 22.3% | 4 |
| Finnishnot grpmax-eligible | 20.2% | 5 |
| African / African-American | 16.1% | 6 |
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.Asp389=
- Coding
- c.1167C>T
- MANE Select
- NM_001752
- dbSNP
- rs769217
- Type
- single nucleotide variant
- Location
- chr11:34461361 (GRCh38)
- Gene constraint
- LOEUF 0.9 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.97 · 17 PDB
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-asp389 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown