Is UTP20 p.Ser201Phe (c.602C>T) pathogenic?

UTP20 p.Ser201Phe (c.602C>T) is classified Uncertain significance in UTP20 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-01). AlphaMissense: likely benign (0.2206); Very rare (popmax 0.00952%, afr).

How common is UTP20 p.Ser201Phe (c.602C>T) in the general population?

UTP20 p.Ser201Phe (c.602C>T) is very rare (popmax 0.00952%, afr) (gnomAD).

What do computational predictors say about UTP20 p.Ser201Phe (c.602C>T)?

AlphaMissense predicts likely benign (score 0.2206) — an in-silico prediction, not a clinical call.

UTP20 p.Ser201Phe

c.602C>T · VCV3814548

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2206 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00952%, afr)

Computational evidence

Protein change
AlphaMissense	0.2206	likely benign
REVEL	0.366	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 2, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 90 kb · p 0.01 · regional, not allelic
Overall
CADD	23.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00952% African / African-American · 7/73,566 alleles

Filtering AF 0.00445% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00313%

Overall 0.000573% 9/1,570,470 alleles · very rare exomes 4/1,418,158 · genomes 5/152,312 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00952%	10,509
Admixed American	0.00177%	56,474
Remaining individualsnot grpmax-eligible	0.00164%	60,936

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: UTP20
Protein: p.Ser201Phe
Coding: c.602C>T
MANE Select: NM_014503
Type: single nucleotide variant
Location: chr12:101290141 (GRCh38)
Gene constraint: LOEUF 0.545 · pLI <0.01 (gnomAD)

Full UTP20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

UTP20 p.Ile1931Thr Uncertain significance ★★ same type
UTP20 c.735+8A>C Benign ★★ same type
UTP20 p.Ala2599= Benign/Likely benign ★★ same type
UTP20 p.His1302= Benign ★★ same type
UTP20 p.His1934Arg Benign ★★ same type
UTP20 p.His304= Benign ★★ same type
UTP20 p.Leu2053= Benign ★★ same type
UTP20 p.Lys1979Glu 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/utp20-p-ser201phe (accessed [today's date]).

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