Is UTP14C p.Leu509= (c.1527G>A) pathogenic?

UTP14C p.Leu509= (c.1527G>A) is classified Likely benign in UTP14C (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-01). Rare (popmax 0.148%, sas).

How common is UTP14C p.Leu509= (c.1527G>A) in the general population?

UTP14C p.Leu509= (c.1527G>A) is rare (popmax 0.148%, sas) (gnomAD).

UTP14C p.Leu509=

c.1527G>A · VCV3388645

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.148%, sas)

⚠ 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 0.59	GERP -2.6, phastCons 0.67
Overall
CADD	0.864	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.148% South Asian · 135/91,086 alleles

Filtering AF 0.128% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.12%

Overall 0.0101% 163/1,614,214 alleles · rare exomes 151/1,461,890 · genomes 12/152,324 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.148%	675
Remaining individualsnot grpmax-eligible	0.0256%	3,907
European (non-Finnish)	0.00102%	98,337

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: UTP14C
Protein: p.Leu509=
Coding: c.1527G>A
MANE Select: NM_021645
Type: single nucleotide variant
Location: chr13:52030331 (GRCh38)

Full UTP14C 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/utp14c-p-leu509 (accessed [today's date]).

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