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NM_198291.3(SRC):c.1579G>A (p.Glu527Lys) AND Thrombocytopenia 6

Germline classification:
Likely pathogenic (2 submissions)
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:
RCV000211002.6

Allele description [Variation Report for NM_198291.3(SRC):c.1579G>A (p.Glu527Lys)]

NM_198291.3(SRC):c.1579G>A (p.Glu527Lys)

Gene:
SRC:SRC proto-oncogene, non-receptor tyrosine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q11.23
Genomic location:
Preferred name:
NM_198291.3(SRC):c.1579G>A (p.Glu527Lys)
HGVS:
  • NC_000020.11:g.37403347G>A
  • NG_023033.1:g.63663G>A
  • NM_005417.5:c.1579G>A
  • NM_198291.3:c.1579G>AMANE SELECT
  • NP_005408.1:p.Glu527Lys
  • NP_005408.1:p.Glu527Lys
  • NP_938033.1:p.Glu527Lys
  • LRG_1018:g.63663G>A
  • NC_000020.10:g.36031750G>A
  • NM_005417.4:c.1579G>A
  • P12931:p.Glu527Lys
Protein change:
E527K; GLU527LYS
Links:
UniProtKB: P12931#VAR_076919; OMIM: 190090.0002; dbSNP: rs879255268
NCBI 1000 Genomes Browser:
rs879255268
Molecular consequence:
  • NM_005417.5:c.1579G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198291.3:c.1579G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Name:
Thrombocytopenia 6 (THC6)
Synonyms:
THROMBOCYTOPENIA, AUTOSOMAL DOMINANT, 6
Identifiers:
MONDO: MONDO:0014837; MedGen: C4310789; OMIM: 616937

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000267654OMIM
no assertion criteria provided
Pathogenic
(Oct 12, 2021)
germlineliterature only

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

SCV002569914ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot provided2yesclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

A dominant gain-of-function mutation in universal tyrosine kinase SRC causes thrombocytopenia, myelofibrosis, bleeding, and bone pathologies.

Turro E, Greene D, Wijgaerts A, Thys C, Lentaigne C, Bariana TK, Westbury SK, Kelly AM, Selleslag D, Stephens JC, Papadia S, Simeoni I, Penkett CJ, Ashford S, Attwood A, Austin S, Bakchoul T, Collins P, Deevi SV, Favier R, Kostadima M, Lambert MP, et al.

Sci Transl Med. 2016 Mar 2;8(328):328ra30. doi: 10.1126/scitranslmed.aad7666. Epub 2016 Mar 2.

PubMed [citation]
PMID:
26936507
PMCID:
PMC5903547

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 OMIM, SCV000267654.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In affected members of a 3-generation family with thrombocytopenia-6 (THC6; 616937), Turro et al. (2016) identified a heterozygous c.1579G-A transition in the SRC gene, resulting in a glu527-to-lys (E527K) substitution at a conserved residue in the kinase domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family and was not found in the ExAC database or in 2,974 in-house control subjects. In vitro functional expression assays showed that the mutation resulted in high kinase activity compared to wildtype, consistent with a dominant gain of function. Immunoblot analysis of patient cells showed increased levels of active SRC and overall increased tyrosine phosphorylation compared to controls. Transfection of the mutation into control blood stem cells caused defective megakaryopoiesis associated with increased overall tyrosine phosphorylation in megakaryocytes. Compared with control conditions, more megakaryocytes were immature and had defects in proplatelet formation, with alterations in the actin cytoskeleton and podosome structures when adhered to fibrinogen. These abnormalities resembled those found in patient bone marrow biopsies and could be rescued using an SRC inhibitor. Expression of the mutation in zebrafish embryos resulted in abnormal early primitive hematopoiesis, thrombocytopenia, and smaller bones compared to controls.

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

From ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology, SCV002569914.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providedyesclinical testing PubMed (2)
2not provided1not providedyesclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided
2germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Mar 26, 2023