DUSP13B p.Val35=
c.105C>T · rs112032940 · VCV780870
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.81%, 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 1.8 | GERP -1.6, phastCons 0.004 |
| Overall | ||
| CADD | 6.659 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.81%
African / African-American · 3,227/67,150 alleles
Filtering AF
4.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.61%
Overall
0.271%
3,621/1,337,402 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.81% | 21 |
| Remaining individualsnot grpmax-eligible | 0.333% | 300 |
| Admixed American | 0.304% | 329 |
| Middle Eastern | 0.107% | 932 |
| South Asian | 0.0167% | 5,979 |
| European (non-Finnish) | 0.00794% | 12,590 |
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
- DUSP13B
- Protein
- p.Val35=
- Coding
- c.105C>T
- MANE Select
- NM_001363514 · reported on NM_001007273
- dbSNP
- rs112032940
- Type
- single nucleotide variant
- Location
- chr10:75103972 (GRCh38)
- Structure
- AlphaFold pLDDT 90.56 · 2 PDB
- Residue 35
- an α-helix
Similar variants
- DUSP13B p.Pro161Gln Uncertain significance ★★ ⚠ same type
- DUSP13B c.582-1G>T Uncertain significance ★ same type
- DUSP13B p.Ala165Thr Uncertain significance ★ ⚠ same type
- DUSP13B p.Ala256Asp Uncertain significance ★ ⚠ same type
- DUSP13B p.Ala262Gly Uncertain significance ★ ⚠ same type
- DUSP13B p.Ala287Asp Uncertain significance ★ ⚠ same type
- DUSP13B p.Arg146Gln Uncertain significance ★ ⚠ same type
- DUSP13B p.Arg169His 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/dusp13b-p-val35 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown