DALRD3 p.Val140=
c.420G>A · rs777652063 · VCV2578944
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00469%, nfe)
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 0.43 | GERP -3.6, phastCons 0.99 |
| Overall | ||
| CADD | 9.697 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00469%
European (non-Finnish) · 53/1,131,052 alleles
Filtering AF
0.00366%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00331%
Overall
0.00382%
57/1,491,866 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00469% | 21,341 |
| Remaining individualsnot grpmax-eligible | 0.00348% | 28,737 |
| African / African-American | 0.0028% | 35,695 |
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
- DALRD3
- Protein
- p.Val140=
- Coding
- c.420G>A
- MANE Select
- NM_001009996
- dbSNP
- rs777652063
- Type
- single nucleotide variant
- Location
- chr3:49018064 (GRCh38)
- Gene constraint
- LOEUF 1.126 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.57
Similar variants
- DALRD3 c.1512+18T>C Benign ★★ same type
- DALRD3 p.Gln299Arg Benign ★★ same type
- DALRD3 p.Gln299Ter Likely pathogenic ★ same type
- DALRD3 c.1329+1G>A Uncertain significance ★ same type
- DALRD3 c.-5T>C Uncertain significance ★ same type
- DALRD3 p.Ala109Ser Uncertain significance ★ ⚠ same type
- DALRD3 p.Ala149Ser Uncertain significance ★ ⚠ same type
- DALRD3 p.Ala14Pro 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/dalrd3-p-val140 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown