FAT4 p.Ser2848=
c.8544C>T · rs139132509 · VCV383607
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 9 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.35%, 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 -2.4 | GERP -4.6 |
| Overall | ||
| CADD | 8.055 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.35%
European (non-Finnish) · 15,897/1,179,408 alleles
Filtering AF
1.33%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.32%
Overall
1.09%
17,579/1,613,226 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.35% | 74 |
| Remaining individualsnot grpmax-eligible | 0.883% | 113 |
| Finnishnot grpmax-eligible | 0.811% | 123 |
| Admixed American | 0.555% | 180 |
| Amishnot grpmax-eligible | 0.548% | 182 |
| African / African-American | 0.196% | 510 |
| Middle Eastern | 0.165% | 605 |
| South Asian | 0.113% | 884 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0372% | 2,689 |
| East Asian | 0.00446% | 22,410 |
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.Ser2848=
- Coding
- c.8544C>T
- MANE Select
- NM_001291303
- dbSNP
- rs139132509
- Type
- single nucleotide variant
- Location
- chr4:125449554 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 (gnomAD)
- Residue 2848
- the cadherin 27 domain
Similar variants
- 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
- FAT4 p.Ala1032Val 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-ser2848 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown