FAT1 p.Pro382=
c.1146C>A · rs371822287 · VCV719388
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.784%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.3 | GERP -4.5 |
| Overall | ||
| CADD | 5.569 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.784%
South Asian · 714/91,072 alleles
Filtering AF
0.736%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.717%
Overall
0.118%
1,899/1,613,806 alleles · rare
exomes 1,772/1,461,538 · genomes 127/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.784% | 128 |
| Middle Eastern | 0.594% | 168 |
| Ashkenazi Jewishnot grpmax-eligible | 0.29% | 344 |
| Remaining individualsnot grpmax-eligible | 0.163% | 613 |
| European (non-Finnish) | 0.0771% | 1,297 |
| Admixed American | 0.055% | 1,819 |
| African / African-American | 0.0213% | 4,690 |
| East Asian | 0.00223% | 44,878 |
| Finnishnot grpmax-eligible | 0.00157% | 63,856 |
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
- FAT1
- Protein
- p.Pro382=
- Coding
- c.1146C>A
- MANE Select
- NM_005245
- dbSNP
- rs371822287
- Type
- single nucleotide variant
- Location
- chr4:186708682 (GRCh38)
- Gene constraint
- LOEUF 0.571 · pLI <0.01 (gnomAD)
- Residue 382
- the cadherin 3 domain
Similar variants
- FAT1 p.Ala1663Thr Uncertain significance ★★ same type
- FAT1 p.Ala1762Val Uncertain significance ★★ ⚠ same type
- FAT1 p.Ala1862Ser Uncertain significance ★★ ⚠ same type
- FAT1 p.Ala2046Thr Uncertain significance ★★ ⚠ same type
- FAT1 p.Ala2456Thr Uncertain significance ★★ ⚠ same type
- FAT1 p.Ala2502Asp Uncertain significance ★★ ⚠ same type
- FAT1 p.Ala3007Val Uncertain significance ★★ same type
- FAT1 p.Ala3437Thr Uncertain significance ★★ ⚠ 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/fat1-p-pro382 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown