Is NEB p.Cys402= (c.1206C>T) pathogenic?

NEB p.Cys402= (c.1206C>T) is classified Conflicting classifications of pathogenicity in NEB (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-01-26). Rare (popmax 0.363%, afr); Associated with nemaline myopathy 2.

What condition is associated with NEB p.Cys402= (c.1206C>T)?

NEB p.Cys402= (c.1206C>T) is associated with nemaline myopathy 2 (ClinVar).

How common is NEB p.Cys402= (c.1206C>T) in the general population?

NEB p.Cys402= (c.1206C>T) is rare (popmax 0.363%, afr) (gnomAD).

How is Severe congenital nemaline myopathy inherited?

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

NEB p.Cys402=

c.1206C>T · rs199695976 · VCV281390

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.363%, afr)

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 -7.7	GERP -4.5
Overall
CADD	0.067	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.363% African / African-American · 272/74,868 alleles

Filtering AF 0.328% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.314%

Overall 0.0235% 379/1,612,896 alleles · rare exomes 192/1,460,776 · genomes 187/152,120 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.363%	275
Remaining individualsnot grpmax-eligible	0.0497%	2,014
Admixed American	0.0452%	2,214
European (non-Finnish)	0.00373%	26,810
South Asian	0.0033%	30,265
Finnishnot grpmax-eligible	0.00313%	31,985

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.Cys402=
Coding: c.1206C>T
MANE Select: NM_001164508
dbSNP: rs199695976
Type: single nucleotide variant
Location: chr2:151697595 (GRCh38)
Gene constraint: LOEUF 0.597 · pLI <0.01 (gnomAD)

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.Cys402Gly 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
NEB p.Ser6366Ile Pathogenic ★★★ same condition
NEB p.Ser6648= 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-cys402 (accessed [today's date]).

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