DUSP13B p.Ala48Val
c.143C>T · rs79802987 · VCV786165
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.62%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.012 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.42 | GERP -4.1 |
| Overall | ||
| CADD | 0.149 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.62%
African / African-American · 2,412/66,630 alleles
Filtering AF
3.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.45%
Overall
0.205%
2,697/1,317,812 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.62% | 28 |
| Admixed American | 0.243% | 412 |
| Remaining individualsnot grpmax-eligible | 0.221% | 452 |
| Middle Eastern | 0.11% | 907 |
| South Asian | 0.0574% | 1,744 |
| European (non-Finnish) | 0.00261% | 38,318 |
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.Ala48Val
- Coding
- c.143C>T
- MANE Select
- NM_001363514 · reported on NM_001007273
- dbSNP
- rs79802987
- Type
- single nucleotide variant
- Location
- chr10:75103934 (GRCh38)
- Structure
- AlphaFold pLDDT 90.56 · 2 PDB
- Residue 48
- the tyrosine-protein phosphatase domain; a β-strand
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-ala48val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown