FUS p.Asp490=
c.1470C>T · rs1299073464 · VCV718229
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, eas)
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 2.7 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 11.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,888 alleles
Filtering AF
0.00726%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00514%
Overall
0.000434%
7/1,613,562 alleles · ultra-rare
exomes 4/1,461,596 · genomes 3/151,966 · joint denominator
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
- FUS
- Protein
- p.Asp490=
- Coding
- c.1470C>T
- MANE Select
- NM_004960
- dbSNP
- rs1299073464
- Type
- single nucleotide variant
- Location
- chr16:31191039 (GRCh38)
- Gene constraint
- LOEUF 0.104 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.96 · 23 PDB
- Residue 490
- the 'disordered' region
Similar variants
- FUS p.Asp490fs Likely pathogenic same residue
- FUS p.Arg481Ter Pathogenic/Likely pathogenic ★★ same type
- FUS p.Arg495Ter Pathogenic ★★ same type
- FUS p.Arg514Gly Pathogenic ★★ ⚠ same type
- FUS p.Arg521Cys Pathogenic ★★ same type
- FUS p.Arg521Gly Pathogenic ★★ same type
- FUS p.Arg521His Pathogenic ★★ ⚠ same type
- FUS p.Arg521Leu Pathogenic/Likely pathogenic ★★ 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/fus-p-asp490 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown