Is UTP14C p.Ala617Val (c.1850C>T) pathogenic?

UTP14C p.Ala617Val (c.1850C>T) is classified Uncertain significance in UTP14C (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-17). AlphaMissense: likely benign (0.11); Ultra-rare (popmax 0.0111%, eas).

How common is UTP14C p.Ala617Val (c.1850C>T) in the general population?

UTP14C p.Ala617Val (c.1850C>T) is ultra-rare (popmax 0.0111%, eas) (gnomAD).

What do computational predictors say about UTP14C p.Ala617Val (c.1850C>T)?

AlphaMissense predicts likely benign (score 0.11) — an in-silico prediction, not a clinical call.

UTP14C p.Ala617Val

c.1850C>T · rs546716607 · VCV2596090

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.11 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0111%, eas)

Missense predictors

0/3 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	0.11	likely benign
REVEL	0.121	moderately benign-leaning
SaProt	LLR -9.99	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Pangolin	Δ0.67	gain · loss 0.00 · independent
Constraint at this position
Conservation	phyloP -0.86	GERP -1.1
Regional constraint	o/e 0.92	unconstrained · MANE · 2,297 bp · p 0.015 · regional, not allelic
Overall
CADD	15.74	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0111% East Asian · 5/44,888 alleles

Filtering AF 0.00434% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00276%

Overall 0.00335% 54/1,613,968 alleles · ultra-rare exomes 51/1,461,870 · genomes 3/152,098 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0111%	8,978
European (non-Finnish)	0.0039%	25,653
Admixed American	0.00167%	59,992
Remaining individualsnot grpmax-eligible	0.0016%	62,490
South Asian	0.0011%	91,084

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.Ala617Val
Coding: c.1850C>T
MANE Select: NM_021645
dbSNP: rs546716607
Type: single nucleotide variant
Location: chr13:52030654 (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-ala617val (accessed [today's date]).

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