NM_019844.4(SLCO1B3):c.484T>G (p.Cys162Gly) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Dec 31, 2019
Review status:: criteria provided, conflicting classifications

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:: RCV000756666.16

Allele description [Variation Report for NM_019844.4(SLCO1B3):c.484T>G (p.Cys162Gly)]

NM_019844.4(SLCO1B3):c.484T>G (p.Cys162Gly)

Genes:

SLCO1B3-SLCO1B7:SLCO1B3-SLCO1B7 readthrough [Gene - HGNC]
SLCO1B3:solute carrier organic anion transporter family member 1B3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p12.2

Genomic location:

Preferred name:

NM_019844.4(SLCO1B3):c.484T>G (p.Cys162Gly)

HGVS:

NC_000012.12:g.20862414T>G
NG_032071.1:g.56711T>G
NM_001349920.2:c.400T>G
NM_019844.4:c.484T>GMANE SELECT
NP_001336849.1:p.Cys134Gly
NP_062818.1:p.Cys162Gly
NC_000012.11:g.21015348T>G
NM_019844.3:c.484T>G

Protein change:

C134G

Links:

dbSNP: rs140353351

NCBI 1000 Genomes Browser:

rs140353351

Molecular consequence:

NM_001349920.2:c.400T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_019844.4:c.484T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Cataglyphis hispanica calcium-independent phospholipase A2-gamma-like...
PREDICTED: Cataglyphis hispanica calcium-independent phospholipase A2-gamma-like (LOC126850714), transcript variant X4, mRNA
gi|2296790274|ref|XM_050593975.1|

Nucleotide
PREDICTED: Chiroxiphia lanceolata ELKS/RAB6-interacting/CAST family member 2 (ER...
PREDICTED: Chiroxiphia lanceolata ELKS/RAB6-interacting/CAST family member 2 (ERC2), transcript variant X7, misc_RNA
gi|1815681169|ref|XR_004359177.1|

Nucleotide
PREDICTED: Chiroxiphia lanceolata monoglyceride lipase (MGLL), transcript varian...
PREDICTED: Chiroxiphia lanceolata monoglyceride lipase (MGLL), transcript variant X5, mRNA
gi|1815681190|ref|XM_032699599.1|

Nucleotide
Homo sapiens transmembrane protein 59 (TMEM59), transcript variant 1, mRNA
Homo sapiens transmembrane protein 59 (TMEM59), transcript variant 1, mRNA
gi|1676439839|ref|NM_001305043.2|

Nucleotide
za77a10.s1 Soares_fetal_lung_NbHL19W Homo sapiens cDNA clone IMAGE:298554 3', mR...
za77a10.s1 Soares_fetal_lung_NbHL19W Homo sapiens cDNA clone IMAGE:298554 3', mRNA sequence
gi|1227172|gnl|dbEST|476686|gb|N705

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000884546	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Uncertain significance (May 3, 2018)	germline	clinical testing	Citation Link,
SCV001023056	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 31, 2019)	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

SCV000884546

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Uncertain significance
(May 3, 2018)

germline

clinical testing

Citation Link,

SCV001023056

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 31, 2019)

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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884546.1

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

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001023056.2

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

#	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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