NM_000433.4(NCF2):c.55_63del (p.Lys19_Asp21del) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 27, 2019
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:: RCV000494542.2

Allele description [Variation Report for NM_000433.4(NCF2):c.55_63del (p.Lys19_Asp21del)]

NM_000433.4(NCF2):c.55_63del (p.Lys19_Asp21del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1q25.3

Genomic location:

Preferred name:

NM_000433.4(NCF2):c.55_63del (p.Lys19_Asp21del)

HGVS:

NC_000001.11:g.183590271_183590279del
NG_007267.1:g.5307_5315del
NM_000433.4:c.55_63delMANE SELECT
NM_001127651.3:c.55_63del
NM_001190789.2:c.55_63del
NM_001190794.2:c.55_63del
NP_000424.2:p.Lys19_Asp21del
NP_000424.2:p.Lys19_Asp21del
NP_001121123.1:p.Lys19_Asp21del
NP_001177718.1:p.Lys19_Asp21del
NP_001177723.1:p.Lys19_Asp21del
LRG_88t1:c.55_63del
LRG_88:g.5307_5315del
LRG_88p1:p.Lys19_Asp21del
NC_000001.10:g.183559402_183559410del
NC_000001.10:g.183559406_183559414del
NM_000433.3:c.55_63del
NM_000433.3:c.55_63delAAGAAGGAC

Links:

OMIM: 608515.0006; dbSNP: rs796065033

NCBI 1000 Genomes Browser:

rs796065033

Molecular consequence:

NM_000433.4:c.55_63del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001127651.3:c.55_63del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001190789.2:c.55_63del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001190794.2:c.55_63del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000582904	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Aug 27, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000582904

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Aug 27, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000582904.4

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

Description

In-frame deletion of 3 amino acids in a non-repeat region; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 18625437, 20167518, 10598813, 10498624, 32040803)

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

Last Updated: Sep 29, 2024

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