Is NMUR2 p.Phe152fs (c.454_458del) pathogenic?

NMUR2 p.Phe152fs (c.454458del) is classified Likely benign in NMUR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-10-24). Rare (popmax 0.209%, afr).

How common is NMUR2 p.Phe152fs (c.454_458del) in the general population?

NMUR2 p.Phe152fs (c.454_458del) is rare (popmax 0.209%, afr) (gnomAD).

NMUR2 p.Phe152fs

c.454_458del · rs370782921 · VCV764859

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.209%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -8.8	GERP -3.7
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.209% African / African-American · 157/75,046 alleles

Filtering AF 0.182% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.172%

Overall 0.0107% 172/1,614,138 alleles · rare exomes 72/1,461,838 · genomes 100/152,300 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.209%	478
Middle Eastern	0.0165%	6,050
Admixed American	0.0117%	8,575
Remaining individualsnot grpmax-eligible	0.0096%	10,418
South Asian	0.0011%	91,080

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.Phe152fs
Coding: c.454_458del
MANE Select: NM_020167
dbSNP: rs370782921
Type: Deletion
Location: chr5:152404656 (GRCh38)
Gene constraint: LOEUF 1.327 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.92 · 3 PDB
Residue 152: an α-helix

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

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-phe152fs (accessed [today's date]).

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