FAT2 p.Ser3463=
c.10389G>A · rs149006704 · VCV2062325
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0546%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.016 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -2.9 | GERP -3.9 |
| Overall | ||
| CADD | 0.189 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0546%
African / African-American · 41/75,044 alleles
Filtering AF
0.0413%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0367%
Overall
0.00452%
73/1,614,160 alleles · ultra-rare
exomes 44/1,461,886 · genomes 29/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0546% | 1,830 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00833% | 12,002 |
| East Asian | 0.00446% | 22,441 |
| European (non-Finnish) | 0.00186% | 53,638 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| South Asian | 0.0011% | 91,084 |
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.Ser3463=
- Coding
- c.10389G>A
- MANE Select
- NM_001447
- dbSNP
- rs149006704
- Type
- single nucleotide variant
- Location
- chr5:151525885 (GRCh38)
- Gene constraint
- LOEUF 0.554 · pLI <0.01 (gnomAD)
- Residue 3463
- the cadherin 31 domain
Similar variants
- FAT2 p.Ser3463Leu Uncertain significance ★ same residue
- 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
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-ser3463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown