Is DPY30 p.Arg98Gln (c.293G>A) pathogenic?

DPY30 p.Arg98Gln (c.293G>A) is classified Uncertain significance in DPY30 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-22). AlphaMissense: ambiguous (0.3644); Very rare (popmax 0.00134%, afr).

How common is DPY30 p.Arg98Gln (c.293G>A) in the general population?

DPY30 p.Arg98Gln (c.293G>A) is very rare (popmax 0.00134%, afr) (gnomAD).

What do computational predictors say about DPY30 p.Arg98Gln (c.293G>A)?

AlphaMissense predicts ambiguous (score 0.3644) — an in-silico prediction, not a clinical call.

DPY30 p.Arg98Gln

c.293G>A · rs958169082 · VCV3085637

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3644 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.3644	ambiguous
REVEL	0.117	moderately benign-leaning
SaProt	LLR -5.09	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 1.9, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 67 bp · p 0.29 · regional, not allelic
Overall
CADD	25.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,866 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000186% 3/1,611,688 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00134%	74,866
European (non-Finnish)	0.00017%	589,456

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: DPY30
Protein: p.Arg98Gln
Coding: c.293G>A
MANE Select: NM_001321209
dbSNP: rs958169082
Type: single nucleotide variant
Location: chr2:32024191 (GRCh38)
Gene constraint: LOEUF 0.747 · pLI 0.46 (gnomAD)
Structure: AlphaFold pLDDT 75.98 · 12 PDB

Full DPY30 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPY30 p.Ala85Val Uncertain significance ★ ⚠ same type
DPY30 p.His18Pro Uncertain significance ★ ⚠ same type
DPY30 p.Phe95Ser Uncertain significance ★ ⚠ same type
DPY30 p.Val31Leu 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/dpy30-p-arg98gln (accessed [today's date]).

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