Is UTP20 p.Pro720= (c.2160G>A) pathogenic?

UTP20 p.Pro720= (c.2160G>A) is classified Benign in UTP20 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-01). Low-frequency (popmax 1.97%, mid).

How common is UTP20 p.Pro720= (c.2160G>A) in the general population?

UTP20 p.Pro720= (c.2160G>A) is low-frequency (popmax 1.97%, mid) (gnomAD).

UTP20 p.Pro720=

c.2160G>A · VCV3904800

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.97%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -7.9	GERP -4.8
Overall
CADD	0.178	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.97% Middle Eastern · 115/5,838 alleles

Filtering AF 1.68% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.57%

Overall 1.32% 21,236/1,613,102 alleles · low-frequency exomes 19,642/1,460,952 · genomes 1,594/152,150 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	4.01%	25
Middle Easterngrpmax	1.97%	51
European (non-Finnish)	1.5%	67
Remaining individualsnot grpmax-eligible	1.39%	72
Admixed American	0.767%	130
Finnishnot grpmax-eligible	0.704%	142
South Asian	0.377%	265
African / African-American	0.228%	438
Amishnot grpmax-eligible	0.11%	912

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro720=
Coding: c.2160G>A
MANE Select: NM_014503
Type: single nucleotide variant
Location: chr12:101309768 (GRCh38)
Gene constraint: LOEUF 0.545 · pLI <0.01 (gnomAD)
Residue 720: an α-helix

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-pro720 (accessed [today's date]).

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