FAT2 p.Pro2198=
c.6594A>G · rs79948184 · VCV786066
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.14%, afr)
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 -4 |
| Overall | ||
| CADD | 1.262 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.14%
African / African-American · 2,354/75,004 alleles
Filtering AF
3.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.99%
Overall
0.167%
2,691/1,613,474 alleles · low-frequency
exomes 1,362/1,461,234 · genomes 1,329/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.14% | 32 |
| Remaining individualsnot grpmax-eligible | 0.235% | 425 |
| Admixed American | 0.175% | 572 |
| Middle Eastern | 0.134% | 745 |
| South Asian | 0.00659% | 15,176 |
| European (non-Finnish) | 0.00602% | 16,614 |
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.Pro2198=
- Coding
- c.6594A>G
- MANE Select
- NM_001447
- dbSNP
- rs79948184
- Type
- single nucleotide variant
- Location
- chr5:151544533 (GRCh38)
- Gene constraint
- LOEUF 0.554 · pLI <0.01 (gnomAD)
- Residue 2198
- the cadherin 19 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-pro2198 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown