FAT2 p.Val1364=
c.4092G>A · rs2304023 · VCV1290500
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 10.6%, 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. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 8.103 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.6%
African / African-American · 7,925/75,042 alleles
Filtering AF
10.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.3%
Overall
1.39%
22,387/1,614,208 alleles · common
exomes 16,793/1,461,880 · genomes 5,594/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.6% | 9 |
| Amishnot grpmax-eligible | 7.02% | 14 |
| East Asian | 6.15% | 16 |
| Finnishnot grpmax-eligible | 2.15% | 47 |
| Remaining individualsnot grpmax-eligible | 1.81% | 55 |
| South Asian | 1.67% | 60 |
| Admixed American | 1.6% | 63 |
| Middle Eastern | 1.27% | 79 |
| Ashkenazi Jewishnot grpmax-eligible | 1.24% | 80 |
| European (non-Finnish) | 0.526% | 190 |
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
- FAT2
- Protein
- p.Val1364=
- Coding
- c.4092G>A
- MANE Select
- NM_001447
- dbSNP
- rs2304023
- Type
- single nucleotide variant
- Location
- chr5:151553241 (GRCh38)
- Gene constraint
- LOEUF 0.554 · pLI <0.01 (gnomAD)
- Residue 1364
- the cadherin 12 domain
Similar variants
- FAT2 p.Ala1009Val Uncertain significance ★★ ⚠ same type
- FAT2 p.Ala1078Thr Uncertain significance ★★ ⚠ same type
- FAT2 p.Ala1079Asp Uncertain significance ★★ ⚠ same type
- FAT2 p.Ala1975Glu Uncertain significance ★★ same type
- FAT2 p.Ala2491Glu Uncertain significance ★★ same type
- FAT2 p.Ala249Val Uncertain significance ★★ ⚠ same type
- FAT2 p.Ala2587Val Uncertain significance ★★ same type
- FAT2 p.Ala2618Thr 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/fat2-p-val1364 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown