FUCA2 p.Asp383=
c.1149T>C · rs113752927 · VCV716073
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.64%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.5 | GERP -3.5 |
| Overall | ||
| CADD | 3.306 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.64%
African / African-American · 1,232/74,958 alleles
Filtering AF
1.57%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.54%
Overall
0.101%
1,628/1,613,012 alleles · low-frequency
exomes 879/1,460,758 · genomes 749/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.64% | 61 |
| Middle Eastern | 0.413% | 242 |
| Remaining individualsnot grpmax-eligible | 0.189% | 529 |
| Admixed American | 0.172% | 582 |
| European (non-Finnish) | 0.0123% | 8,133 |
| South Asian | 0.0055% | 18,197 |
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
- FUCA2
- Protein
- p.Asp383=
- Coding
- c.1149T>C
- MANE Select
- NM_032020
- dbSNP
- rs113752927
- Type
- single nucleotide variant
- Location
- chr6:143501937 (GRCh38)
- Gene constraint
- LOEUF 1.015 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.89
Similar variants
- FUCA2 p.Phe184Leu Uncertain significance ★★ ⚠ same type
- FUCA2 p.Ala168Asp Uncertain significance ★ ⚠ same type
- FUCA2 p.Ala28Val Uncertain significance ★ ⚠ same type
- FUCA2 p.Ala43Val Uncertain significance ★ ⚠ same type
- FUCA2 p.Ala462Gly Uncertain significance ★ ⚠ same type
- FUCA2 p.Arg176Cys Uncertain significance ★ ⚠ same type
- FUCA2 p.Arg202Trp Uncertain significance ★ ⚠ same type
- FUCA2 p.Arg254Gln 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/fuca2-p-asp383 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown