NM_000433.4(NCF2):c.1165C>A (p.His389Asn) AND Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 20, 2022
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:: RCV001217928.7

Allele description [Variation Report for NM_000433.4(NCF2):c.1165C>A (p.His389Asn)]

NM_000433.4(NCF2):c.1165C>A (p.His389Asn)

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.1165C>A (p.His389Asn)

HGVS:

NC_000001.11:g.183563447G>T
NG_007267.1:g.32135C>A
NM_000433.4:c.1165C>AMANE SELECT
NM_001127651.3:c.1165C>A
NM_001190789.2:c.922C>A
NM_001190794.2:c.1030C>A
NP_000424.2:p.His389Asn
NP_001121123.1:p.His389Asn
NP_001177718.1:p.His308Asn
NP_001177723.1:p.His344Asn
LRG_88t1:c.1165C>A
LRG_88:g.32135C>A
NC_000001.10:g.183532582G>T
NM_000433.3:c.1165C>A

Protein change:

H308N

Links:

dbSNP: rs201325416

NCBI 1000 Genomes Browser:

rs201325416

Molecular consequence:

NM_000433.4:c.1165C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127651.3:c.1165C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001190789.2:c.922C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001190794.2:c.1030C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2
Synonyms:: CGD, AUTOSOMAL RECESSIVE CYTOCHROME b-POSITIVE, TYPE II; GRANULOMATOUS DISEASE, CHRONIC, DUE TO NCF2 DEFICIENCY; GRANULOMATOUS DISEASE, CHRONIC, AUTOSOMAL RECESSIVE, 2
Identifiers:: MONDO: MONDO:0009310; MedGen: C1856245; Orphanet: 379; OMIM: 233710

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001389789	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 20, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001389789

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 20, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001389789.4

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

Description

This sequence change replaces histidine, which is basic and polar, with asparagine, which is neutral and polar, at codon 389 of the NCF2 protein (p.His389Asn). This variant is present in population databases (rs201325416, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with NCF2-related conditions. ClinVar contains an entry for this variant (Variation ID: 946961). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

ClinVar

Relating variation to medicine