Is NEB p.Pro4407= (c.13221G>A) pathogenic?

NEB p.Pro4407= (c.13221G>A) is classified Likely benign in NEB (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-11). Ultra-rare (popmax 0.0687%, mid); Associated with nemaline myopathy 2.

What condition is associated with NEB p.Pro4407= (c.13221G>A)?

NEB p.Pro4407= (c.13221G>A) is associated with nemaline myopathy 2 (ClinVar).

How common is NEB p.Pro4407= (c.13221G>A) in the general population?

NEB p.Pro4407= (c.13221G>A) is ultra-rare (popmax 0.0687%, mid) (gnomAD).

How is Severe congenital nemaline myopathy inherited?

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

NEB p.Pro4407=

c.13221G>A · rs1240952464 · VCV534090

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0687%, mid)

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 -20	GERP -3.7
Overall
CADD	4.496	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0687% Middle Eastern · 3/4,364 alleles

Filtering AF 0.0187% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00994%

Overall 0.00311% 48/1,544,270 alleles · ultra-rare exomes 44/1,396,606 · genomes 4/147,664 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0687%	1,455
Remaining individualsnot grpmax-eligible	0.00669%	14,955
East Asian	0.00491%	20,366
South Asian	0.00358%	27,945
European (non-Finnish)	0.00288%	34,699
African / African-American	0.00283%	35,322
Admixed American	0.00198%	50,630

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.Pro4407=
Coding: c.13221G>A
MANE Select: NM_001164508
dbSNP: rs1240952464
Type: single nucleotide variant
Location: chr2:151603611 (GRCh38)
Gene constraint: LOEUF 0.597 · pLI <0.01 (gnomAD)
Residue 4407: 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.Pro4407fs Pathogenic/Likely pathogenic ★★ same residue
NEB p.Pro4407Arg 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-pro4407 (accessed [today's date]).

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