FAT4 p.Val376=
c.1128G>A · rs202216461 · VCV388300
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.637%, nfe)
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 4.4 | GERP 0.64, phastCons 1 |
| Overall | ||
| CADD | 12.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.637%
European (non-Finnish) · 7,522/1,180,002 alleles
Filtering AF
0.625%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.62%
Overall
0.506%
8,159/1,613,874 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.637% | 157 |
| Remaining individualsnot grpmax-eligible | 0.483% | 207 |
| Admixed American | 0.212% | 473 |
| Finnishnot grpmax-eligible | 0.183% | 545 |
| African / African-American | 0.105% | 950 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0338% | 2,961 |
| South Asian | 0.0022% | 45,531 |
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
- FAT4
- Protein
- p.Val376=
- Coding
- c.1128G>A
- MANE Select
- NM_001291303
- dbSNP
- rs202216461
- Type
- single nucleotide variant
- Location
- chr4:125317539 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 (gnomAD)
- Residue 376
- a β-strand; the cadherin 4 domain
Similar variants
- FAT4 p.Val376Leu Uncertain significance ★ same residue
- FAT4 p.Arg1902Ter Pathogenic/Likely pathogenic ★★ same type
- FAT4 p.Arg2234Ter Pathogenic/Likely pathogenic ★★ same type
- FAT4 p.Gln4530Ter Pathogenic/Likely pathogenic ★★ same type
- FAT4 p.Glu2502Ter Pathogenic/Likely pathogenic ★★ same type
- FAT4 c.5307+6T>A Uncertain significance ★★ same type
- FAT4 c.6843+4A>G Uncertain significance ★★ same type
- FAT4 p.Ala1020Val 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/fat4-p-val376 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown