FAT2 p.Arg1469=
c.4405C>A · rs35884212 · VCV2083996
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.524%, sas)
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 7.4 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 7.844 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.524%
South Asian · 477/91,056 alleles
Filtering AF
0.485%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.47%
Overall
0.0507%
819/1,614,048 alleles · rare
exomes 770/1,461,838 · genomes 49/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.524% | 191 |
| Middle Eastern | 0.364% | 275 |
| Ashkenazi Jewishnot grpmax-eligible | 0.105% | 955 |
| Remaining individualsnot grpmax-eligible | 0.0848% | 1,179 |
| Admixed American | 0.0483% | 2,069 |
| European (non-Finnish) | 0.0172% | 5,813 |
| African / African-American | 0.00533% | 18,751 |
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.Arg1469=
- Coding
- c.4405C>A
- MANE Select
- NM_001447
- dbSNP
- rs35884212
- Type
- single nucleotide variant
- Location
- chr5:151550763 (GRCh38)
- Gene constraint
- LOEUF 0.554 · pLI <0.01 (gnomAD)
- Residue 1469
- the cadherin 13 domain
Similar variants
- FAT2 p.Arg1469Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- FAT2 p.Arg1469Ter 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
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-arg1469 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown