FAT1 p.Ser4367=
c.13101T>C · rs1298865 · VCV1273862
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 67.1%, afr) — 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. | ||
| REVEL | 0.121 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.41 | GERP -2.9, phastCons 0.005 |
| Overall | ||
| CADD | 3.289 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
67.1%
African / African-American · 50,306/74,934 alleles
Filtering AF
66.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 66.4%
Overall
38.6%
623,313/1,613,448 alleles · common
exomes 551,315/1,461,412 · genomes 71,998/152,036 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 67.1% | 1 |
| East Asian | 64.2% | 2 |
| Admixed American | 56.5% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 45.9% | 2 |
| Middle Eastern | 40.9% | 2 |
| Remaining individualsnot grpmax-eligible | 39.8% | 3 |
| Finnishnot grpmax-eligible | 38.6% | 3 |
| European (non-Finnish) | 35.7% | 3 |
| Amishnot grpmax-eligible | 30.8% | 3 |
| South Asian | 25.9% | 4 |
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.Ser4367=
- Coding
- c.13101T>C
- MANE Select
- NM_005245
- dbSNP
- rs1298865
- Type
- single nucleotide variant
- Location
- chr4:186595726 (GRCh38)
- Gene constraint
- LOEUF 0.571 · pLI <0.01 (gnomAD)
- Residue 4367
- the 'disordered' region
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-ser4367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown