Is NEB p.Gln59= (c.177G>A) pathogenic?

NEB p.Gln59= (c.177G>A) is classified Conflicting classifications of pathogenicity in NEB (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2026-04-01). Rare (popmax 0.318%, amr); Associated with nemaline myopathy 2.

What condition is associated with NEB p.Gln59= (c.177G>A)?

NEB p.Gln59= (c.177G>A) is associated with nemaline myopathy 2 (ClinVar).

How common is NEB p.Gln59= (c.177G>A) in the general population?

NEB p.Gln59= (c.177G>A) is rare (popmax 0.318%, amr) (gnomAD).

How is Severe congenital nemaline myopathy inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

NEB p.Gln59=

c.177G>A · rs200990309 · VCV331542

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

rare (popmax 0.318%, amr)

Conditions

nemaline myopathy 2

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 -0.74	GERP -0.037, phastCons 0.037
Overall
CADD	0.401	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.318% Admixed American · 189/59,346 alleles

Filtering AF 0.281% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.267%

Overall 0.115% 1,838/1,599,154 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.318%	314
European (non-Finnish)	0.13%	770
Remaining individualsnot grpmax-eligible	0.116%	859
African / African-American	0.0455%	2,200
Finnishnot grpmax-eligible	0.0331%	3,022
South Asian	0.0011%	91,038

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: NEB
Protein: p.Gln59=
Coding: c.177G>A
MANE Select: NM_001164508
dbSNP: rs200990309
Type: single nucleotide variant
Location: chr2:151727808 (GRCh38)
Gene constraint: LOEUF 0.597 · pLI <0.01 (gnomAD)
Residue 59: the 'disordered' region

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

Disease context

nemaline myopathy 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Severe congenital nemaline myopathy (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

NEB p.Gln59Ter Pathogenic ★★ same residue
NEB p.Gln59Glu Uncertain significance ★ ⚠ same residue
NEB p.Gln59His Uncertain significance ★ ⚠ same residue
NEB c.11910+1G>A Likely pathogenic ★★★ same condition
NEB c.6076-1G>T Likely pathogenic ★★★ same condition
NEB c.78+1G>A Pathogenic ★★★ same condition
NEB p.Arg2313Ter Pathogenic ★★★ same condition
NEB p.Asp498Gly Likely pathogenic ★★★ ⚠ same condition

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/neb-p-gln59 (accessed [today's date]).

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