Is NCF2 p.Ser347fs (c.1038_1039del) pathogenic?

NCF2 p.Ser347fs (c.10381039del) is classified Pathogenic in NCF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-18). No gnomAD frequency available for this variant; Associated with granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2.

What condition is associated with NCF2 p.Ser347fs (c.1038_1039del)?

NCF2 p.Ser347fs (c.1038_1039del) is associated with granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2 (ClinVar).

How common is NCF2 p.Ser347fs (c.1038_1039del) in the general population?

NCF2 p.Ser347fs (c.1038_1039del) is no gnomAD frequency available for this variant (gnomAD).

How is Chronic granulomatous disease inherited?

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

NCF2 p.Ser347fs

c.1038_1039del · rs2527911236 · VCV2734054

Pathogenic Single submitter

Classification

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

granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 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 12 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.22	GERP -0.43

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: NCF2
Protein: p.Ser347fs
Coding: c.1038_1039del
MANE Select: NM_000433
dbSNP: rs2527911236
Type: Deletion
Location: chr1:183563573 (GRCh38)
Gene constraint: LOEUF 0.799 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.99 · 7 PDB

Full NCF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Chronic granulomatous disease (Orphanet):

Inheritance: Autosomal recessive, X-linked recessive
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

NCF2 p.Ala140fs Pathogenic/Likely pathogenic ★★ same condition
NCF2 p.Lys19_Asp21del Pathogenic ★★ same condition
NCF2 p.Lys391fs Pathogenic ★★ same condition
NCF2 p.Thr279fs Pathogenic ★★ same condition
NCF2 c.258-13del Likely benign ★★ same condition
NCF2 c.855+20del Likely benign ★★ same condition
NCF2 p.Gln367fs Likely pathogenic ★ same condition
NCF2 p.Glu243fs 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/ncf2-p-ser347fs (accessed [today's date]).

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