Is DDX54 p.Pro337= (c.1011C>G) pathogenic?

DDX54 p.Pro337= (c.1011C>G) is classified Likely benign in DDX54 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-04). Absent from gnomAD v4.1.

How common is DDX54 p.Pro337= (c.1011C>G) in the general population?

DDX54 p.Pro337= (c.1011C>G) is absent from gnomAD v4.1 (gnomAD).

DDX54 p.Pro337=

c.1011C>G · VCV4918695

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.28	GERP -4, phastCons 0.018
Overall
CADD	6.217	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DDX54
Protein: p.Pro337=
Coding: c.1011C>G
MANE Select: NM_024072
Type: single nucleotide variant
Location: chr12:113174697 (GRCh38)
Gene constraint: LOEUF 0.821 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.89 · 6 PDB
Residue 337: the helicase c-terminal domain; a β-strand

Full DDX54 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DDX54 p.Gln608His Uncertain significance ★★ ⚠ same type
DDX54 p.Ser71Leu Uncertain significance ★★ ⚠ same type
DDX54 c.937-5C>T Benign/Likely benign ★★ same type
DDX54 p.Asp132= Benign ★★ same type
DDX54 p.Ala148Thr Uncertain significance ★ ⚠ same type
DDX54 p.Ala169Ser Uncertain significance ★ ⚠ same type
DDX54 p.Ala169Val Uncertain significance ★ ⚠ same type
DDX54 p.Ala258Thr 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/ddx54-p-pro337 (accessed [today's date]).

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