Is NEB p.Gln2012= (c.6036G>A) pathogenic?

NEB p.Gln2012= (c.6036G>A) is classified Likely benign in NEB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-11). Very rare (popmax 0.00167%, amr); Associated with nemaline myopathy 2.

What condition is associated with NEB p.Gln2012= (c.6036G>A)?

NEB p.Gln2012= (c.6036G>A) is associated with nemaline myopathy 2 (ClinVar).

How common is NEB p.Gln2012= (c.6036G>A) in the general population?

NEB p.Gln2012= (c.6036G>A) is very rare (popmax 0.00167%, 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.Gln2012=

c.6036G>A · rs770061515 · VCV2176066

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

nemaline myopathy 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.8	GERP 2.3, phastCons 1
Overall
CADD	9.831	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,966 alleles

Overall 0.000124% 2/1,612,762 alleles · very rare exomes 1/1,460,682 · genomes 1/152,080 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,966
European (non-Finnish)	8.48e-05%	1,179,076

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.Gln2012=
Coding: c.6036G>A
MANE Select: NM_001164508
dbSNP: rs770061515
Type: single nucleotide variant
Location: chr2:151659104 (GRCh38)
Gene constraint: LOEUF 0.597 · pLI <0.01 (gnomAD)
Residue 2012: a UniProt-annotated variant site (in amc6)

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.Gln2012Arg Uncertain significance ★ ⚠ same residue
NEB p.Gln2012His Likely benign ★ 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
NEB p.Ser6366Ile 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-gln2012 (accessed [today's date]).

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