SORT1 p.Phe198=
c.594T>C · rs11142 · VCV3059274
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 97.1%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
SORT1-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 3.4 | GERP 0.73, phastCons 1 |
| Overall | ||
| CADD | 9.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
97.1%
East Asian · 43,549/44,862 alleles
Filtering AF
96.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 96%
Overall
73.1%
1,179,375/1,612,478 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 97.1% | 1 |
| Admixed American | 85.6% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 84.1% | 1 |
| Middle Eastern | 78.5% | 1 |
| Remaining individualsnot grpmax-eligible | 74.3% | 1 |
| South Asian | 73.3% | 1 |
| European (non-Finnish) | 71.7% | 1 |
| Finnishnot grpmax-eligible | 71.1% | 1 |
| African / African-American | 68% | 1 |
| Amishnot grpmax-eligible | 65.9% | 2 |
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
- SORT1
- Protein
- p.Phe198=
- Coding
- c.594T>C
- MANE Select
- NM_002959
- dbSNP
- rs11142
- Type
- single nucleotide variant
- Location
- chr1:109354481 (GRCh38)
- Gene constraint
- LOEUF 0.553 · pLI 0.83 (gnomAD)
- Structure
- AlphaFold pLDDT 83.27 · 17 PDB
- Residue 198
- the '10-bladed beta-propeller' region; a disulfide bond; the vps10p domain; a β-strand
Disease context
SORT1-related disorder
Similar variants
- SORT1 c.544-5A>G Likely benign same condition
- SORT1 p.Ile763= Likely benign same condition
- SORT1 p.Pro4= Benign same condition
- SORT1 p.Pro747= Likely benign same condition
- SORT1 p.Ser409= Likely benign same condition
- SORT1 p.Ser540= Benign same condition
- SORT1 p.Thr323= Benign same condition
- SORT1 p.Asp358Tyr 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/sort1-p-phe198 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown