Is UNC45A p.Pro939= (c.2817C>A) pathogenic?

UNC45A p.Pro939= (c.2817C>A) is classified Likely benign in UNC45A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-09). Very rare (popmax 0.00212%, nfe).

How common is UNC45A p.Pro939= (c.2817C>A) in the general population?

UNC45A p.Pro939= (c.2817C>A) is very rare (popmax 0.00212%, nfe) (gnomAD).

UNC45A p.Pro939=

c.2817C>A · VCV4694756

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00212%, nfe)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.18	GERP -0.24, phastCons 0.77
Overall
CADD	7.775	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00212% European (non-Finnish) · 25/1,179,938 alleles

Filtering AF 0.00145% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00123%

Overall 0.00155% 25/1,613,904 alleles · very rare exomes 25/1,461,560 · genomes 0/152,344 · joint denominator

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: UNC45A
Protein: p.Pro939=
Coding: c.2817C>A
MANE Select: NM_018671
Type: single nucleotide variant
Location: chr15:90953698 (GRCh38)

Full UNC45A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/unc45a-p-pro939 (accessed [today's date]).

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