SUMF1 p.Val166=
c.498G>A · rs2469991702 · VCV2784597
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
mucosulfatidosis
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP 0.63, phastCons 1 |
| Overall | ||
| CADD | 10.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SUMF1
- Protein
- p.Val166=
- Coding
- c.498G>A
- MANE Select
- NM_182760
- dbSNP
- rs2469991702
- Type
- single nucleotide variant
- Location
- chr3:4449287 (GRCh38)
- Gene constraint
- LOEUF 1.254 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.39 · 21 PDB
Disease context
mucosulfatidosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Multiple sulfatase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Antenatal, Childhood, Infancy, Neonatal
Similar variants
- SUMF1 c.271-1G>C Likely pathogenic ★★ same condition
- SUMF1 c.445-1G>A Pathogenic/Likely pathogenic ★★ same condition
- SUMF1 c.445-2A>G Pathogenic/Likely pathogenic ★★ same condition
- SUMF1 c.520-1G>C Likely pathogenic ★★ same condition
- SUMF1 c.602+1G>A Pathogenic/Likely pathogenic ★★ same condition
- SUMF1 c.603-1G>C Pathogenic ★★ same condition
- SUMF1 c.840+1G>A Likely pathogenic ★★ same condition
- SUMF1 c.954+1G>T Likely pathogenic ★★ same condition
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/sumf1-p-val166 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown