NM_020297.4(ABCC9):c.2599G>A (p.Val867Ile) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: May 6, 2019
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000756944.10

Allele description [Variation Report for NM_020297.4(ABCC9):c.2599G>A (p.Val867Ile)]

NM_020297.4(ABCC9):c.2599G>A (p.Val867Ile)

Gene:

ABCC9:ATP binding cassette subfamily C member 9 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p12.1

Genomic location:

Preferred name:

NM_020297.4(ABCC9):c.2599G>A (p.Val867Ile)

HGVS:

NC_000012.12:g.21852412C>T
NG_012819.1:g.89283G>A
NM_001377273.1:c.2599G>A
NM_001377274.1:c.1732G>A
NM_005691.2:c.2599G>A
NM_005691.4:c.2599G>A
NM_020297.4:c.2599G>AMANE SELECT
NP_001364202.1:p.Val867Ile
NP_001364203.1:p.Val578Ile
NP_005682.2:p.Val867Ile
NP_005682.2:p.Val867Ile
NP_064693.2:p.Val867Ile
LRG_377t2:c.2599G>A
LRG_377:g.89283G>A
NC_000012.11:g.22005346C>T
NM_005691.3:c.2599G>A
NM_020297.2:c.2599G>A

Protein change:

V578I

Links:

dbSNP: rs376754153

NCBI 1000 Genomes Browser:

rs376754153

Molecular consequence:

NM_001377273.1:c.2599G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001377274.1:c.1732G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005691.4:c.2599G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020297.4:c.2599G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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PREDICTED: Rattus norvegicus torsin family 1, member B (Tor1b), transcript varia...
PREDICTED: Rattus norvegicus torsin family 1, member B (Tor1b), transcript variant X2, mRNA
gi|2678930164|ref|XM_063283960.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000884937	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Uncertain significance (Aug 18, 2017)	germline	clinical testing	Citation Link,
SCV001993717	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 6, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000884937

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Uncertain significance
(Aug 18, 2017)

germline

clinical testing

Citation Link,

SCV001993717

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 6, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884937.1

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

Description

The c.2599G>A; p.Val867Ile variant (rs376754153) has not been reported in the medical literature nor has it been previously identified by our laboratory. This variant is listed in the Genome Aggregation Database (gnomAD) with an overall population frequency of 0.002 percent (identified on 5 out of 276,842 chromosomes), and is reported to the ClinVar database as a variant of uncertain significance (Variation ID: 410821). The valine at position 867 is moderately conserved considering 12 species (Alamut v2.9.0) and computational analyses of the effects of the p.Val867Ile variant on protein structure and function indicates conflicting results (SIFT: tolerated, MutationTaster: disease causing, PolyPhen-2: benign). Altogether, there is not enough evidence to classify the p.Val867Ile variant with certainty.

#	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

From GeneDx, SCV001993717.2

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

Description

Has not been previously published as pathogenic or benign to our knowledge; 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 that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 31983221)

#	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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