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NM_000433.4(NCF2):c.4T>G (p.Ser2Ala) AND Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 19, 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:
RCV003091115.2

Allele description [Variation Report for NM_000433.4(NCF2):c.4T>G (p.Ser2Ala)]

NM_000433.4(NCF2):c.4T>G (p.Ser2Ala)

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.4T>G (p.Ser2Ala)
HGVS:
  • NC_000001.11:g.183590326A>C
  • NG_007267.1:g.5256T>G
  • NM_000433.4:c.4T>GMANE SELECT
  • NM_001127651.3:c.4T>G
  • NM_001190789.2:c.4T>G
  • NM_001190794.2:c.4T>G
  • NM_001410895.1:c.4T>G
  • NP_000424.2:p.Ser2Ala
  • NP_000424.2:p.Ser2Ala
  • NP_001121123.1:p.Ser2Ala
  • NP_001177718.1:p.Ser2Ala
  • NP_001177723.1:p.Ser2Ala
  • NP_001397824.1:p.Ser2Ala
  • LRG_88t1:c.4T>G
  • LRG_88:g.5256T>G
  • LRG_88p1:p.Ser2Ala
  • NC_000001.10:g.183559461A>C
  • NM_000433.3:c.4T>G
Protein change:
S2A
Molecular consequence:
  • NM_000433.4:c.4T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127651.3:c.4T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001190789.2:c.4T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001190794.2:c.4T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001410895.1:c.4T>G - 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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003469115Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 19, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003469115.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces serine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 2 of the NCF2 protein (p.Ser2Ala). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with NCF2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024