FAT1 p.Arg3=
c.9A>G · rs371512264 · VCV2723420
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0508%, afr)
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 -0.14 | GERP -3.3, phastCons 0.15 |
| Overall | ||
| CADD | 2.664 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0508%
African / African-American · 38/74,814 alleles
Filtering AF
0.038%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0335%
Overall
0.00293%
47/1,601,530 alleles · ultra-rare
exomes 21/1,449,312 · genomes 26/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0508% | 1,969 |
| Middle Eastern | 0.0166% | 6,012 |
| Remaining individualsnot grpmax-eligible | 0.00966% | 10,351 |
| Admixed American | 0.00342% | 29,234 |
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.Arg3=
- Coding
- c.9A>G
- MANE Select
- NM_005245
- dbSNP
- rs371512264
- Type
- single nucleotide variant
- Location
- chr4:186709819 (GRCh38)
- Gene constraint
- LOEUF 0.571 · pLI <0.01 (gnomAD)
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-arg3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown