FUT4 p.Pro300=
c.900C>T · rs540852486 · VCV722197
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0517%, sas)
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 -1.5 | GERP -3.3 |
| Overall | ||
| CADD | 7.064 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0517%
South Asian · 47/90,938 alleles
Filtering AF
0.0399%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0357%
Overall
0.00317%
51/1,611,252 alleles · ultra-rare
exomes 39/1,458,890 · genomes 12/152,362 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0517% | 1,935 |
| European (non-Finnish) | 0.000339% | 294,711 |
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.Pro300=
- Coding
- c.900C>T
- MANE Select
- NM_002033
- dbSNP
- rs540852486
- Type
- single nucleotide variant
- Location
- chr11:94545033 (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.Pro54= 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
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-pro300 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown