Is UTP14C p.Arg230Trp (c.688C>T) pathogenic?

UTP14C p.Arg230Trp (c.688C>T) is classified Uncertain significance in UTP14C (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-12). AlphaMissense: likely benign (0.1669); Very rare (popmax 0.00668%, afr).

How common is UTP14C p.Arg230Trp (c.688C>T) in the general population?

UTP14C p.Arg230Trp (c.688C>T) is very rare (popmax 0.00668%, afr) (gnomAD).

What do computational predictors say about UTP14C p.Arg230Trp (c.688C>T)?

AlphaMissense predicts likely benign (score 0.1669) — an in-silico prediction, not a clinical call.

UTP14C p.Arg230Trp

c.688C>T · VCV3331702

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1669 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00668%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

⚠ 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	0.1669	likely benign
REVEL	0.34	indeterminate
SaProt	LLR -13.70	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.42	GERP -0.082, phastCons 0.028
Regional constraint	o/e 0.92	unconstrained · MANE · 2,297 bp · p 0.015 · regional, not allelic
Overall
CADD	23.7	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 0.00668% African / African-American · 5/74,878 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00191%

Overall 0.00266% 43/1,613,982 alleles · very rare exomes 38/1,461,890 · genomes 5/152,092 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00668%	14,976
Remaining individualsnot grpmax-eligible	0.0032%	31,244
European (non-Finnish)	0.00297%	33,716
Finnishnot grpmax-eligible	0.00156%	64,020

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.Arg230Trp
Coding: c.688C>T
MANE Select: NM_021645
Type: single nucleotide variant
Location: chr13:52029492 (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-arg230trp (accessed [today's date]).

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