Is NMUR2 p.Val272= (c.816C>T) pathogenic?

NMUR2 p.Val272= (c.816C>T) is classified Benign in NMUR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-02-08). Common (popmax 6.66%, afr) — too common for a highly-penetrant pathogenic allele.

NMUR2 p.Val272=

Q: How common is NMUR2 p.Val272= (c.816C>T) in the general population?

NMUR2 p.Val272= (c.816C>T) is common (popmax 6.66%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.816C>T · rs10055345 · VCV780588

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 6.66%, afr) — too common for a highly-penetrant pathogenic allele

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 0.44	GERP -3.8, phastCons 0.78
Overall
CADD	3.926	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.66% African / African-American · 4,984/74,838 alleles

Filtering AF 6.51% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.44%

Overall 0.345% 5,561/1,613,184 alleles · common exomes 2,768/1,461,300 · genomes 2,793/151,884 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	6.66%	15
Remaining individualsnot grpmax-eligible	0.435%	230
Admixed American	0.384%	260
Middle Eastern	0.281%	356
South Asian	0.0176%	5,688
European (non-Finnish)	0.00356%	28,087

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: NMUR2
Protein: p.Val272=
Coding: c.816C>T
MANE Select: NM_020167
dbSNP: rs10055345
Type: single nucleotide variant
Location: chr5:152395580 (GRCh38)
Gene constraint: LOEUF 1.327 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.92 · 3 PDB
Residue 272: an α-helix

Full NMUR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

NMUR2 p.Ala124Val Uncertain significance ★ ⚠ same type
NMUR2 p.Ala132Val Uncertain significance ★ ⚠ same type
NMUR2 p.Ala147Thr Uncertain significance ★ same type
NMUR2 p.Ala154Val Uncertain significance ★ ⚠ same type
NMUR2 p.Ala395Glu Uncertain significance ★ ⚠ same type
NMUR2 p.Arg108His Uncertain significance ★ ⚠ same type
NMUR2 p.Arg153Leu Uncertain significance ★ ⚠ same type
NMUR2 p.Arg162Trp 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/nmur2-p-val272 (accessed [today's date]).

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