NM_000433.4(NCF2):c.230G>A (p.Arg77Gln) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 10, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004689402.1

Allele description [Variation Report for NM_000433.4(NCF2):c.230G>A (p.Arg77Gln)]

NM_000433.4(NCF2):c.230G>A (p.Arg77Gln)

Gene:

NCF2:neutrophil cytosolic factor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q25.3

Genomic location:

Preferred name:

NM_000433.4(NCF2):c.230G>A (p.Arg77Gln)

HGVS:

NC_000001.11:g.183586922C>T
NG_007267.1:g.8660G>A
NM_000433.4:c.230G>AMANE SELECT
NM_001127651.3:c.230G>A
NM_001190789.2:c.230G>A
NM_001190794.2:c.230G>A
NP_000424.2:p.Arg77Gln
NP_000424.2:p.Arg77Gln
NP_001121123.1:p.Arg77Gln
NP_001177718.1:p.Arg77Gln
NP_001177723.1:p.Arg77Gln
LRG_88t1:c.230G>A
LRG_88:g.8660G>A
LRG_88p1:p.Arg77Gln
NC_000001.10:g.183556057C>T
NM_000433.3:c.230G>A
NM_000433.4:c.230G>A
P19878:p.Arg77Gln

Protein change:

R77Q; ARG77GLN

Links:

UniProtKB: P19878#VAR_017388; UniProtKB/Swiss-Prot: VAR_017388; OMIM: 608515.0008; dbSNP: rs119103275

NCBI 1000 Genomes Browser:

rs119103275

Molecular consequence:

NM_000433.4:c.230G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127651.3:c.230G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001190789.2:c.230G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001190794.2:c.230G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005184946	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (May 10, 2024)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21190454, 10598813 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005184946

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(May 10, 2024)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Residual NADPH oxidase and survival in chronic granulomatous disease.

Kuhns DB, Alvord WG, Heller T, Feld JJ, Pike KM, Marciano BE, Uzel G, DeRavin SS, Priel DA, Soule BP, Zarember KA, Malech HL, Holland SM, Gallin JI.

N Engl J Med. 2010 Dec 30;363(27):2600-10. doi: 10.1056/NEJMoa1007097.

PubMed [citation]

PMID:: 21190454
PMCID:: PMC3069846

Autosomal recessive chronic granulomatous disease caused by novel mutations in NCF-2, the gene encoding the p67-phox component of phagocyte NADPH oxidase.

Noack D, Rae J, Cross AR, Muñoz J, Salmen S, Mendoza JA, Rossi N, Curnutte JT, Heyworth PG.

Hum Genet. 1999 Nov;105(5):460-7.

PubMed [citation]

PMID:: 10598813

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005184946.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: NCF2 c.230G>A (p.Arg77Gln) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251494 control chromosomes. c.230G>A has been reported in the literature in compound heterozygous individuals affected with Chronic Granulomatous Disease (e.g. Kuhns_2011, Noack_1999). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 21190454, 10598813). ClinVar contains an entry for this variant (Variation ID: 2247). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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