FAT4 p.Pro1098=
c.3294T>A · rs200300207 · VCV509829
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.252%, 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 0.18 | GERP 0.91, phastCons 0.99 |
| Overall | ||
| CADD | 7.296 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.252%
European (non-Finnish) · 2,971/1,179,904 alleles
Filtering AF
0.244%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.241%
Overall
0.192%
3,097/1,614,086 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.252% | 397 |
| Remaining individualsnot grpmax-eligible | 0.0944% | 1,059 |
| African / African-American | 0.0466% | 2,145 |
| Ashkenazi Jewishnot grpmax-eligible | 0.027% | 3,700 |
| Admixed American | 0.02% | 5,003 |
| Middle Eastern | 0.0165% | 6,062 |
| Finnishnot grpmax-eligible | 0.0141% | 7,116 |
| South Asian | 0.0022% | 45,541 |
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.Pro1098=
- Coding
- c.3294T>A
- MANE Select
- NM_001291303
- dbSNP
- rs200300207
- Type
- single nucleotide variant
- Location
- chr4:125319705 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 (gnomAD)
- Residue 1098
- the cadherin 10 domain
Similar variants
- FAT4 p.Pro1098Ala 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-pro1098 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown