Is OTUD5 p.Pro25= (c.75G>C) pathogenic?

OTUD5 p.Pro25= (c.75G>C) is classified Likely benign in OTUD5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-05-08). Absent from gnomAD v4.1; Associated with OTUD5-related disorder.

What condition is associated with OTUD5 p.Pro25= (c.75G>C)?

OTUD5 p.Pro25= (c.75G>C) is associated with OTUD5-related disorder (ClinVar).

How common is OTUD5 p.Pro25= (c.75G>C) in the general population?

OTUD5 p.Pro25= (c.75G>C) is absent from gnomAD v4.1 (gnomAD).

OTUD5 p.Pro25=

c.75G>C · VCV3357830

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

OTUD5-related disorder

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 -1.3	GERP -1.9
Overall
CADD	11.04	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: OTUD5
Protein: p.Pro25=
Coding: c.75G>C
MANE Select: NM_001136157
Type: single nucleotide variant
Location: chrX:48957496 (GRCh38)
Structure: AlphaFold pLDDT 66.15 · 3 PDB
Residue 25: the 'disordered' region

Full OTUD5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

OTUD5-related disorder

Similar variants

OTUD5 p.Ser367Leu Likely pathogenic ★ same condition
OTUD5 p.Thr366Pro Uncertain significance ⚠ same condition
OTUD5 p.Arg227= Likely benign same condition
OTUD5 p.Pro23= Likely benign same condition
OTUD5 p.Val36= Likely benign same condition
OTUD5 p.Gly42_Gly48del Conflicting classifications of pathogenicity ★ same condition
OTUD5 p.Arg515Trp Likely pathogenic ★★ ⚠ same type
OTUD5 p.Ala487Val 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/otud5-p-pro25 (accessed [today's date]).

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