Is UTP18 p.Asp213Val (c.638A>T) pathogenic?

UTP18 p.Asp213Val (c.638A>T) is classified Uncertain significance in UTP18 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-16). AlphaMissense: likely benign (0.1242); Very rare (popmax 0.00669%, afr).

How common is UTP18 p.Asp213Val (c.638A>T) in the general population?

UTP18 p.Asp213Val (c.638A>T) is very rare (popmax 0.00669%, afr) (gnomAD).

What do computational predictors say about UTP18 p.Asp213Val (c.638A>T)?

AlphaMissense predicts likely benign (score 0.1242) — an in-silico prediction, not a clinical call.

UTP18 p.Asp213Val

c.638A>T · rs199983161 · VCV2307439

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1242 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00669%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1242	likely benign
REVEL	0.181	moderately benign-leaning
SaProt	LLR -10.36	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 36 kb · p 0.025 · regional, not allelic
Overall
CADD	25.6	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 0.00669% African / African-American · 5/74,756 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00162%

Overall 0.000621% 10/1,609,862 alleles · very rare exomes 5/1,457,748 · genomes 5/152,114 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00669%	14,951
South Asian	0.0011%	90,560
European (non-Finnish)	0.00034%	294,523

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: UTP18
Protein: p.Asp213Val
Coding: c.638A>T
MANE Select: NM_016001
dbSNP: rs199983161
Type: single nucleotide variant
Location: chr17:51273377 (GRCh38)
Gene constraint: LOEUF 0.838 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.92 · 3 PDB
Residue 213: the 'disordered' region

Full UTP18 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

UTP18 p.Asp213Gly Uncertain significance ★ ⚠ same residue
UTP18 p.Ala244Gly Uncertain significance ★ ⚠ same type
UTP18 p.Ala369Thr Uncertain significance ★ ⚠ same type
UTP18 p.Ala432Thr Uncertain significance ★ ⚠ same type
UTP18 p.Ala468Gly Uncertain significance ★ ⚠ same type
UTP18 p.Arg159Trp Uncertain significance ★ ⚠ same type
UTP18 p.Arg161Gln Uncertain significance ★ ⚠ same type
UTP18 p.Arg161Pro Uncertain significance ★ ⚠ 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/utp18-p-asp213val (accessed [today's date]).

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