FAT2 p.Pro1342=
c.4026G>A · rs150507279 · VCV1923396
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -2.2 | GERP -4.4 |
| Overall | ||
| CADD | 1.494 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.00173%
28/1,614,252 alleles · ultra-rare
exomes 24/1,461,884 · genomes 4/152,368 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Admixed American | 0.00666% | 15,006 |
| African / African-American | 0.004% | 25,023 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,254 |
| East Asian | 0.00223% | 44,892 |
| European (non-Finnish) | 0.00144% | 69,414 |
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.Pro1342=
- Coding
- c.4026G>A
- MANE Select
- NM_001447
- dbSNP
- rs150507279
- Type
- single nucleotide variant
- Location
- chr5:151553307 (GRCh38)
- Gene constraint
- LOEUF 0.554 · pLI <0.01 (gnomAD)
- Residue 1342
- the cadherin 11 domain
Similar variants
- FAT2 p.Pro1342Leu 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-pro1342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown