DALRD3 p.Thr81=
c.243C>A · VCV4962550
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0207%, 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 -2.1 | GERP -4 |
| Overall | ||
| CADD | 6.788 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0207%
South Asian · 14/67,596 alleles
Filtering AF
0.0125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00996%
Overall
0.00104%
15/1,437,780 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0207% | 4,828 |
| Remaining individualsnot grpmax-eligible | 0.0018% | 55,456 |
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.Thr81=
- Coding
- c.243C>A
- MANE Select
- NM_001009996
- Type
- single nucleotide variant
- Location
- chr3:49018241 (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-thr81 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown