Is DALRD3 p.Thr32= (c.96C>A) pathogenic?

DALRD3 p.Thr32= (c.96C>A) is classified Likely benign in DALRD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-01). Ultra-rare (popmax 0.0718%, nfe).

How common is DALRD3 p.Thr32= (c.96C>A) in the general population?

DALRD3 p.Thr32= (c.96C>A) is ultra-rare (popmax 0.0718%, nfe) (gnomAD).

DALRD3 p.Thr32=

c.96C>A · rs375207499 · VCV2653816

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0718%, 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 0.27	GERP -1.3, phastCons 0.95
Overall
CADD	11.53	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0718% European (non-Finnish) · 838/1,167,880 alleles

Filtering AF 0.0677% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0661%

Overall 0.0647% 1,028/1,588,824 alleles · ultra-rare exomes 941/1,436,542 · genomes 87/152,282 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.158%	632
Finnishnot grpmax-eligible	0.126%	794
European (non-Finnish)grpmax	0.0718%	1,394
Remaining individualsnot grpmax-eligible	0.0537%	1,862
South Asian	0.0227%	4,402
Admixed American	0.0122%	8,164
African / African-American	0.0107%	9,307

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Thr32=
Coding: c.96C>A
MANE Select: NM_001009996
dbSNP: rs375207499
Type: single nucleotide variant
Location: chr3:49018469 (GRCh38)
Gene constraint: LOEUF 1.126 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.57

Full DALRD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-thr32 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown