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NM_019844.4(SLCO1B3):c.83A>C (p.Lys28Thr) AND Rotor syndrome

Germline classification:
Uncertain significance (1 submission)
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:
RCV003337788.3

Allele description [Variation Report for NM_019844.4(SLCO1B3):c.83A>C (p.Lys28Thr)]

NM_019844.4(SLCO1B3):c.83A>C (p.Lys28Thr)

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.83A>C (p.Lys28Thr)
HGVS:
  • NC_000012.12:g.20815821A>C
  • NG_032071.2:g.10118A>C
  • NM_001371097.1:c.83A>C
  • NM_019844.4:c.83A>CMANE SELECT
  • NP_001358026.1:p.Lys28Thr
  • NP_062818.1:p.Lys28Thr
  • NC_000012.11:g.20968755A>C
  • NG_032071.1:g.10118A>C
Protein change:
K28T
Molecular consequence:
  • NM_001371097.1:c.83A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_019844.4:c.83A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Rotor syndrome (HBLRR)
Synonyms:
Hyperbilirubinemia, Rotor type; HYPERBILIRUBINEMIA, ROTOR TYPE, DIGENIC
Identifiers:
MONDO: MONDO:0009379; MedGen: C0220991; Orphanet: 3111; OMIM: 237450

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004048070Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significancegermlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004048070.1

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

Description

The missense c.83A>C (p.Lys28Thr) variant in SLCO1B3 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is reported with the allele frequency 0.0008% in the gnomAD and novel in 1000 genome database. The amino acid Lys at position 28 is changed to a Thr changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Lys28Thr in SLCO1B3 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance. In the absence of second reportable variant , the molecular diagnosis is not confirmed.

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

Last Updated: Sep 1, 2024