Is NMUR1 p.Arg179Cys (c.535C>T) pathogenic?

NMUR1 p.Arg179Cys (c.535C>T) is classified Benign in NMUR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-26). AlphaMissense: likely benign (0.1083); Rare (popmax 0.946%, afr).

How common is NMUR1 p.Arg179Cys (c.535C>T) in the general population?

NMUR1 p.Arg179Cys (c.535C>T) is rare (popmax 0.946%, afr) (gnomAD).

What do computational predictors say about NMUR1 p.Arg179Cys (c.535C>T)?

AlphaMissense predicts likely benign (score 0.1083) — an in-silico prediction, not a clinical call.

NMUR1 p.Arg179Cys

c.535C>T · rs113464185 · VCV787243

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1083 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.946%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1083	likely benign
REVEL	0.267	benign-leaning
SaProt	LLR -9.45	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 2.1, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 5,315 bp · p 0.033 · regional, not allelic
Overall
CADD	24.4	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 0.946% African / African-American · 710/75,068 alleles

Filtering AF 0.888% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.865%

Overall 0.0522% 843/1,613,654 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.946%	106
Middle Eastern	0.0825%	1,212
Admixed American	0.07%	1,429
Remaining individualsnot grpmax-eligible	0.0608%	1,645
East Asian	0.029%	3,453
South Asian	0.00329%	30,357
European (non-Finnish)	0.00271%	36,876

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: NMUR1
Protein: p.Arg179Cys
Coding: c.535C>T
MANE Select: NM_006056
dbSNP: rs113464185
Type: single nucleotide variant
Location: chr2:231528486 (GRCh38)
Gene constraint: LOEUF 1.399 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.23 · 2 PDB
Residue 179: a disulfide bond; an α-helix

Full NMUR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

NMUR1 p.Arg259Trp Benign/Likely benign ★★ same type
NMUR1 p.Ala176Val Uncertain significance ★ ⚠ same type
NMUR1 p.Ala236Val Uncertain significance ★ ⚠ same type
NMUR1 p.Ala25Thr Uncertain significance ★ ⚠ same type
NMUR1 p.Ala269Val Uncertain significance ★ ⚠ same type
NMUR1 p.Ala350Val Uncertain significance ★ ⚠ same type
NMUR1 p.Ala412Ser Uncertain significance ★ ⚠ same type
NMUR1 p.Arg159His 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/nmur1-p-arg179cys (accessed [today's date]).

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