DENND4B p.Val10=
c.30G>A · rs372779027 · VCV2639364
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.612%, sas)
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 4 | phastCons 1 |
| Overall | ||
| CADD | 12.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.612%
South Asian · 554/90,506 alleles
Filtering AF
0.57%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.553%
Overall
0.207%
3,326/1,608,674 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.612% | 163 |
| Ashkenazi Jewishnot grpmax-eligible | 0.255% | 392 |
| Middle Eastern | 0.248% | 403 |
| European (non-Finnish) | 0.208% | 480 |
| Remaining individualsnot grpmax-eligible | 0.161% | 622 |
| Finnishnot grpmax-eligible | 0.137% | 731 |
| Admixed American | 0.0403% | 2,478 |
| African / African-American | 0.0254% | 3,944 |
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
- DENND4B
- Protein
- p.Val10=
- Coding
- c.30G>A
- MANE Select
- NM_014856
- dbSNP
- rs372779027
- Type
- single nucleotide variant
- Location
- chr1:153944345 (GRCh38)
- Gene constraint
- LOEUF 0.527 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.32
Similar variants
- DENND4B p.Val10Ala Uncertain significance ★ ⚠ same residue
- DENND4B p.Arg561Trp Uncertain significance ★★ ⚠ same type
- DENND4B p.Val103Ile Uncertain significance ★★ ⚠ same type
- DENND4B p.Ala1089Val Uncertain significance ★ ⚠ same type
- DENND4B p.Ala1113Val Uncertain significance ★ ⚠ same type
- DENND4B p.Ala1408Val Uncertain significance ★ ⚠ same type
- DENND4B p.Ala150Thr Uncertain significance ★ ⚠ same type
- DENND4B p.Ala16Thr 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/dennd4b-p-val10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown