Is UTS2R p.Ser245Phe (c.734C>T) pathogenic?

UTS2R p.Ser245Phe (c.734C>T) is classified Likely benign in UTS2R (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-01). AlphaMissense: likely benign (0.2251); Low-frequency (popmax 1.16%, mid).

How common is UTS2R p.Ser245Phe (c.734C>T) in the general population?

UTS2R p.Ser245Phe (c.734C>T) is low-frequency (popmax 1.16%, mid) (gnomAD).

What do computational predictors say about UTS2R p.Ser245Phe (c.734C>T)?

AlphaMissense predicts likely benign (score 0.2251) — an in-silico prediction, not a clinical call.

UTS2R p.Ser245Phe

c.734C>T · rs199914220 · VCV2648495

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2251 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.16%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2251	likely benign
REVEL	0.19	benign-leaning
SaProt	LLR -8.27	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.21	GERP -1.6
Regional constraint	o/e 1.16	unconstrained · MANE · 1,166 bp · p 0.00013 · regional, not allelic
Overall
CADD	18.85	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 1.16% Middle Eastern · 55/4,742 alleles

Filtering AF 0.915% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.827%

Overall 0.0995% 1,414/1,421,024 alleles · low-frequency exomes 1,179/1,268,994 · genomes 235/152,030 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	1.16%	86
Ashkenazi Jewishnot grpmax-eligible	1.08%	92
Amishnot grpmax-eligible	0.881%	114
Admixed American	0.575%	174
Remaining individualsnot grpmax-eligible	0.303%	330
African / African-American	0.108%	926
South Asian	0.0643%	1,555
European (non-Finnish)	0.0579%	1,726

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: UTS2R
Protein: p.Ser245Phe
Coding: c.734C>T
MANE Select: NM_018949
dbSNP: rs199914220
Type: single nucleotide variant
Location: chr17:82375058 (GRCh38)
Structure: AlphaFold pLDDT 77.21 · 2 PDB

Full UTS2R gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

UTS2R p.Leu32= Benign ★★ same type
UTS2R p.Thr181= Benign ★★ same type
UTS2R p.Val121Leu Benign ★★ same type

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/uts2r-p-ser245phe (accessed [today's date]).

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