FUT4 p.Pro54=
c.162A>C · rs190868751 · VCV776650
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.88%, 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 -6.2 | GERP -2 |
| Overall | ||
| CADD | 1.473 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.88%
African / African-American · 3,444/70,518 alleles
Filtering AF
4.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.69%
Overall
0.249%
3,899/1,563,300 alleles · low-frequency
exomes 1,878/1,411,082 · genomes 2,021/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.88% | 20 |
| Remaining individualsnot grpmax-eligible | 0.322% | 310 |
| Admixed American | 0.291% | 344 |
| Middle Eastern | 0.259% | 386 |
| South Asian | 0.0115% | 8,680 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00713% | 14,024 |
| European (non-Finnish) | 0.00638% | 15,677 |
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
- FUT4
- Protein
- p.Pro54=
- Coding
- c.162A>C
- MANE Select
- NM_002033
- dbSNP
- rs190868751
- Type
- single nucleotide variant
- Location
- chr11:94544295 (GRCh38)
- Gene constraint
- LOEUF 1.216 · pLI 0.07 (gnomAD)
- Structure
- AlphaFold pLDDT 74.21
Similar variants
- FUT4 p.Asp516Glu Likely benign ★★ same type
- FUT4 p.Ala119Thr Uncertain significance ★ ⚠ same type
- FUT4 p.Ala120Gly Uncertain significance ★ ⚠ same type
- FUT4 p.Ala128Val Uncertain significance ★ ⚠ same type
- FUT4 p.Ala14Gly Uncertain significance ★ ⚠ same type
- FUT4 p.Ala14Ser Uncertain significance ★ ⚠ same type
- FUT4 p.Ala157Pro Uncertain significance ★ ⚠ same type
- FUT4 p.Ala204Pro 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/fut4-p-pro54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown