Is DDX10 p.Pro44Arg (c.131C>G) pathogenic?

DDX10 p.Pro44Arg (c.131C>G) is classified Likely benign in DDX10 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2017-09-29). AlphaMissense: likely benign (0.1936); Rare (popmax 0.268%, nfe).

How common is DDX10 p.Pro44Arg (c.131C>G) in the general population?

DDX10 p.Pro44Arg (c.131C>G) is rare (popmax 0.268%, nfe) (gnomAD).

What do computational predictors say about DDX10 p.Pro44Arg (c.131C>G)?

AlphaMissense predicts likely benign (score 0.1936) — an in-silico prediction, not a clinical call.

DDX10 p.Pro44Arg

c.131C>G · rs149622934 · VCV777859

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1936 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.268%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1936	likely benign
REVEL	0.112	moderately benign-leaning
SaProt	LLR -9.82	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.4	GERP 2, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 28 kb · p 0.0021 · regional, not allelic
Overall
CADD	26.0	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 0.268% European (non-Finnish) · 3,154/1,177,358 alleles

Filtering AF 0.26% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.257%

Overall 0.248% 3,981/1,607,396 alleles · rare exomes 3,670/1,455,032 · genomes 311/152,364 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.51%	66
Remaining individualsnot grpmax-eligible	0.273%	366
European (non-Finnish)grpmax	0.268%	373
Finnishnot grpmax-eligible	0.148%	674
Admixed American	0.102%	980
African / African-American	0.055%	1,817
Middle Eastern	0.0331%	3,021
South Asian	0.0133%	7,502
East Asian	0.00227%	44,086

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: DDX10
Protein: p.Pro44Arg
Coding: c.131C>G
MANE Select: NM_004398
dbSNP: rs149622934
Type: single nucleotide variant
Location: chr11:108665284 (GRCh38)
Gene constraint: LOEUF 0.86 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.85 · 1 PDB

Full DDX10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DDX10 p.Pro44Ser Uncertain significance ★ ⚠ same residue
DDX10 p.Glu445Gly Benign ★★ same type
DDX10 p.Tyr282= Benign/Likely benign ★★ same type
DDX10 p.Ala154Thr Uncertain significance ★ ⚠ same type
DDX10 p.Ala367Val Uncertain significance ★ same type
DDX10 p.Ala468Ser Uncertain significance ★ ⚠ same type
DDX10 p.Ala537Thr Uncertain significance ★ ⚠ same type
DDX10 p.Ala599Gly 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/ddx10-p-pro44arg (accessed [today's date]).

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