Is UTP14C p.Leu465= (c.1393T>C) pathogenic?

UTP14C p.Leu465= (c.1393T>C) is classified Likely benign in UTP14C (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-01). Ultra-rare (popmax 0.0902%, nfe).

How common is UTP14C p.Leu465= (c.1393T>C) in the general population?

UTP14C p.Leu465= (c.1393T>C) is ultra-rare (popmax 0.0902%, nfe) (gnomAD).

UTP14C p.Leu465=

c.1393T>C · rs41292796 · VCV1694705

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0902%, 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 -0.38	GERP -3.7
Overall
CADD	1.633	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0902% European (non-Finnish) · 1,064/1,180,002 alleles

Filtering AF 0.0856% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0839%

Overall 0.0706% 1,140/1,613,828 alleles · ultra-rare exomes 1,069/1,461,890 · genomes 71/151,938 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0902%	1,109
Remaining individualsnot grpmax-eligible	0.0592%	1,689
Finnishnot grpmax-eligible	0.0438%	2,284
African / African-American	0.00935%	10,690
East Asian	0.00446%	22,446
Admixed American	0.00334%	29,981

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.Leu465=
Coding: c.1393T>C
MANE Select: NM_021645
dbSNP: rs41292796
Type: single nucleotide variant
Location: chr13:52030197 (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-leu465 (accessed [today's date]).

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