Is NEB p.Ile1007fs (c.3018_3019insCATCT) pathogenic?

NEB p.Ile1007fs (c.30183019insCATCT) is classified Likely pathogenic in NEB (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-29). No gnomAD frequency available for this variant; Associated with nemaline myopathy 2.

What condition is associated with NEB p.Ile1007fs (c.3018_3019insCATCT)?

NEB p.Ile1007fs (c.3018_3019insCATCT) is associated with nemaline myopathy 2 (ClinVar).

How common is NEB p.Ile1007fs (c.3018_3019insCATCT) in the general population?

NEB p.Ile1007fs (c.3018_3019insCATCT) is no gnomAD frequency available for this variant (gnomAD).

How is Severe congenital nemaline myopathy inherited?

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

NEB p.Ile1007fs

c.3018_3019insCATCT · rs2552263993 · VCV1725986

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

nemaline myopathy 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 30 of 182
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.1	GERP 0.92, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: NEB
Protein: p.Ile1007fs
Coding: c.3018_3019insCATCT
MANE Select: NM_001164508
dbSNP: rs2552263993
Type: Insertion
Location: chr2:151680753 (GRCh38)
Gene constraint: LOEUF 0.597 · pLI <0.01 (gnomAD)
Residue 1007: 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.Arg6077fs Pathogenic/Likely pathogenic ★★ same condition
NEB c.11077-20_11077-19insC Benign/Likely benign ★★ same condition
NEB c.13476+16_13476+17insG Likely benign ★★ same condition
NEB c.18696_18697insSVAelement Pathogenic ★ same condition
NEB p.Ala7452fs Likely pathogenic ★ same condition
NEB p.Arg6235fs Likely pathogenic ★ same condition
NEB p.Arg6884fs Likely pathogenic ★ same condition
NEB p.Asp2813Ter 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-ile1007fs (accessed [today's date]).

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