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NM_000313.4(PROS1):c.1528G>A (p.Val510Met) AND Thrombophilia due to protein S deficiency, autosomal dominant

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
May 28, 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:
RCV000148749.8

Allele description [Variation Report for NM_000313.4(PROS1):c.1528G>A (p.Val510Met)]

NM_000313.4(PROS1):c.1528G>A (p.Val510Met)

Gene:
PROS1:protein S [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q11.1
Genomic location:
Preferred name:
NM_000313.4(PROS1):c.1528G>A (p.Val510Met)
HGVS:
  • NC_000003.12:g.93879279C>T
  • NG_009813.1:g.99812G>A
  • NM_000313.4:c.1528G>AMANE SELECT
  • NM_001314077.2:c.1624G>A
  • NP_000304.2:p.Val510Met
  • NP_000304.2:p.Val510Met
  • NP_001301006.1:p.Val542Met
  • LRG_572t1:c.1528G>A
  • LRG_572:g.99812G>A
  • LRG_572p1:p.Val510Met
  • NC_000003.11:g.93598123C>T
  • NM_000313.3:c.1528G>A
Protein change:
V510M
Links:
dbSNP: rs138925964
NCBI 1000 Genomes Browser:
rs138925964
Molecular consequence:
  • NM_000313.4:c.1528G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001314077.2:c.1624G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Thrombophilia due to protein S deficiency, autosomal dominant (THPH5)
Identifiers:
MONDO: MONDO:0012868; MedGen: C3278211; Orphanet: 743; OMIM: 612336

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000190486CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation
no assertion criteria provided
Likely benign
(Jun 1, 2014)
germlineresearch

SCV000298014Russ Altman Lab, Stanford University
no assertion criteria provided
risk factor
(May 1, 2015)
somaticresearch, case-control

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

SCV001136555Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Benign
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV002569211ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significancegermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedresearch
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
African Americanssomaticyes221not provided679yesresearch, case-control

Citations

PubMed

Population-specific single-nucleotide polymorphism confers increased risk of venous thromboembolism in African Americans.

Daneshjou R, Cavallari LH, Weeke PE, Karczewski KJ, Drozda K, Perera MA, Johnson JA, Klein TE, Bustamante CD, Roden DM, Shaffer C, Denny JC, Zehnder JL, Altman RB.

Mol Genet Genomic Med. 2016 Sep;4(5):513-20. doi: 10.1002/mgg3.226.

PubMed [citation]
PMID:
27652279
PMCID:
PMC5023936

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 CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation, SCV000190486.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Russ Altman Lab, Stanford University, SCV000298014.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1African Americans3not providedyesresearch PubMed (1)
2African Americans19not providednocase-control PubMed (1)

Description

All family members had the variant.

Case control analysis with p = 0.0041, OR = 4.62, 95% CI: 1.51 – 15.20; allele frequencies – cases: 2.45%, controls: 0.54%

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1somaticyes3Bloodnot provided3not provided1not provided
2somaticyes676Bloodnot provided19not providednot providednot provided

From Mendelics, SCV001136555.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology, SCV002569211.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 23, 2024