Is UTP14C p.Arg672Cys (c.2014C>T) pathogenic?

UTP14C p.Arg672Cys (c.2014C>T) is classified Uncertain significance in UTP14C (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-08). AlphaMissense: likely benign (0.1233); Ultra-rare (popmax 0.0461%, sas).

How common is UTP14C p.Arg672Cys (c.2014C>T) in the general population?

UTP14C p.Arg672Cys (c.2014C>T) is ultra-rare (popmax 0.0461%, sas) (gnomAD).

What do computational predictors say about UTP14C p.Arg672Cys (c.2014C>T)?

AlphaMissense predicts likely benign (score 0.1233) — an in-silico prediction, not a clinical call.

UTP14C p.Arg672Cys

c.2014C>T · rs370985603 · VCV2597400

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1233 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0461%, sas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

⚠ 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
AlphaMissense	0.1233	likely benign
REVEL	0.076	moderately benign-leaning
SaProt	LLR -12.51	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.24	GERP 1.8
Regional constraint	o/e 0.92	unconstrained · MANE · 2,297 bp · p 0.015 · regional, not allelic
Overall
CADD	17.63	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0461% South Asian · 42/91,064 alleles

Filtering AF 0.035% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0311%

Overall 0.0039% 63/1,614,094 alleles · ultra-rare exomes 57/1,461,892 · genomes 6/152,202 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0461%	2,168
Middle Eastern	0.0165%	6,062
Remaining individualsnot grpmax-eligible	0.008%	12,501
Admixed American	0.00666%	15,004
Finnishnot grpmax-eligible	0.00156%	64,022
African / African-American	0.00133%	74,994
European (non-Finnish)	0.000763%	131,114

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.Arg672Cys
Coding: c.2014C>T
MANE Select: NM_021645
dbSNP: rs370985603
Type: single nucleotide variant
Location: chr13:52030818 (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-arg672cys (accessed [today's date]).

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