Is DDX55 p.Pro18Ser (c.52C>T) pathogenic?

DDX55 p.Pro18Ser (c.52C>T) is classified Uncertain significance in DDX55 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-23). AlphaMissense: likely benign (0.0741); Absent from gnomAD v4.1.

How common is DDX55 p.Pro18Ser (c.52C>T) in the general population?

DDX55 p.Pro18Ser (c.52C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DDX55 p.Pro18Ser (c.52C>T)?

AlphaMissense predicts likely benign (score 0.0741) — an in-silico prediction, not a clinical call.

DDX55 p.Pro18Ser

c.52C>T · rs2547792598 · VCV2329460

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0741 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,573,926)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0741	likely benign
REVEL	0.041	moderately benign-leaning
SaProt	LLR -7.36	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.7	GERP 1.6, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 18 kb · p 0.36 · regional, not allelic
Overall
CADD	20.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,573,926). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DDX55
Protein: p.Pro18Ser
Coding: c.52C>T
MANE Select: NM_020936
dbSNP: rs2547792598
Type: single nucleotide variant
Location: chr12:123602200 (GRCh38)
Gene constraint: LOEUF 1.009 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.56

Full DDX55 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DDX55 p.Pro18Ala Uncertain significance ★ ⚠ same residue
DDX55 p.Ala153Asp Uncertain significance ★ ⚠ same type
DDX55 p.Ala215Val Uncertain significance ★ ⚠ same type
DDX55 p.Ala235Val Uncertain significance ★ ⚠ same type
DDX55 p.Ala38Thr Uncertain significance ★ ⚠ same type
DDX55 p.Ala401Pro Uncertain significance ★ ⚠ same type
DDX55 p.Ala456Pro Uncertain significance ★ ⚠ same type
DDX55 p.Arg144Cys 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/ddx55-p-pro18ser (accessed [today's date]).

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