FAT1 p.Arg3420=
c.10260A>G · rs74424517 · VCV767986
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.16%, nfe)
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 0.44 | GERP -2.2, phastCons 0.99 |
| Overall | ||
| CADD | 5.355 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.16%
European (non-Finnish) · 13,667/1,179,480 alleles
Filtering AF
1.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.14%
Overall
0.981%
15,812/1,612,322 alleles · low-frequency
exomes 14,612/1,461,610 · genomes 1,200/150,712 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.16% | 86 |
| Remaining individualsnot grpmax-eligible | 1.03% | 97 |
| Admixed American | 0.93% | 108 |
| Middle Eastern | 0.928% | 108 |
| Ashkenazi Jewishnot grpmax-eligible | 0.872% | 115 |
| South Asian | 0.414% | 241 |
| African / African-American | 0.221% | 452 |
| Finnishnot grpmax-eligible | 0.117% | 853 |
| East Asian | 0.0335% | 2,981 |
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.Arg3420=
- Coding
- c.10260A>G
- MANE Select
- NM_005245
- dbSNP
- rs74424517
- Type
- single nucleotide variant
- Location
- chr4:186606160 (GRCh38)
- Gene constraint
- LOEUF 0.571 · pLI <0.01 (gnomAD)
- Residue 3420
- the cadherin 31 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-arg3420 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown