Is NEB p.Pro331Arg (c.992C>G) pathogenic?

NEB p.Pro331Arg (c.992C>G) is classified Conflicting classifications of pathogenicity in NEB (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2023-10-24). AlphaMissense: ambiguous (0.4064); Very rare (popmax 0.00306%, nfe); Associated with nemaline myopathy 2.

What condition is associated with NEB p.Pro331Arg (c.992C>G)?

NEB p.Pro331Arg (c.992C>G) is associated with nemaline myopathy 2 (ClinVar).

How common is NEB p.Pro331Arg (c.992C>G) in the general population?

NEB p.Pro331Arg (c.992C>G) is very rare (popmax 0.00306%, nfe) (gnomAD).

How is Severe congenital nemaline myopathy inherited?

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

What do computational predictors say about NEB p.Pro331Arg (c.992C>G)?

AlphaMissense predicts ambiguous (score 0.4064) — an in-silico prediction, not a clinical call.

NEB p.Pro331Arg

c.992C>G · rs763822076 · VCV659348

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

ambiguous

0.4064 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00306%, nfe)

Conditions

nemaline myopathy 2

Computational evidence

Protein change
AlphaMissense	0.4064	ambiguous
REVEL	0.727	pathogenic-leaning
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 82 kb · p 0.26 · regional, not allelic
Overall
CADD	24.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00306% European (non-Finnish) · 36/1,175,376 alleles

Filtering AF 0.00224% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00199%

Overall 0.00455% 73/1,605,262 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0472%	2,118
Remaining individualsnot grpmax-eligible	0.0113%	8,883
European (non-Finnish)grpmax	0.00306%	32,649

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro331Arg
Coding: c.992C>G
MANE Select: NM_001164508
dbSNP: rs763822076
Type: single nucleotide variant
Location: chr2:151709699 (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.Pro331= Likely benign ★ same residue
NEB p.Pro331Leu 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

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-pro331arg (accessed [today's date]).

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