Is UTP20 p.Val2115= (c.6345G>A) pathogenic?

UTP20 p.Val2115= (c.6345G>A) is classified Benign in UTP20 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). Low-frequency (popmax 1.34%, nfe).

How common is UTP20 p.Val2115= (c.6345G>A) in the general population?

UTP20 p.Val2115= (c.6345G>A) is low-frequency (popmax 1.34%, nfe) (gnomAD).

UTP20 p.Val2115=

c.6345G>A · rs113954350 · VCV771182

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.34%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.38	GERP -1.1, phastCons 0.012
Overall
CADD	4.286	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.34% European (non-Finnish) · 15,753/1,179,644 alleles

Filtering AF 1.32% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.31%

Overall 1.19% 19,144/1,613,602 alleles · low-frequency exomes 17,788/1,461,402 · genomes 1,356/152,200 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	3.11%	32
Finnishnot grpmax-eligible	1.69%	59
European (non-Finnish)grpmax	1.34%	75
Amishnot grpmax-eligible	1.1%	91
Remaining individualsnot grpmax-eligible	0.954%	105
Admixed American	0.788%	127
Middle Eastern	0.479%	209
African / African-American	0.212%	472
South Asian	0.132%	759

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.Val2115=
Coding: c.6345G>A
MANE Select: NM_014503
dbSNP: rs113954350
Type: single nucleotide variant
Location: chr12:101367937 (GRCh38)
Gene constraint: LOEUF 0.545 · pLI <0.01 (gnomAD)
Residue 2115: 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-val2115 (accessed [today's date]).

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