NM_000313.4(PROS1):c.1762A>G (p.Thr588Ala) AND Thrombophilia due to protein S deficiency, autosomal dominant

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Apr 27, 2017
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:: RCV000148750.7

Allele description [Variation Report for NM_000313.4(PROS1):c.1762A>G (p.Thr588Ala)]

NM_000313.4(PROS1):c.1762A>G (p.Thr588Ala)

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.1762A>G (p.Thr588Ala)

HGVS:

NC_000003.12:g.93877074T>C
NG_009813.1:g.102017A>G
NM_000313.4:c.1762A>GMANE SELECT
NM_001314077.2:c.1858A>G
NP_000304.2:p.Thr588Ala
NP_000304.2:p.Thr588Ala
NP_001301006.1:p.Thr620Ala
LRG_572t1:c.1762A>G
LRG_572:g.102017A>G
LRG_572p1:p.Thr588Ala
NC_000003.11:g.93595918T>C
NM_000313.3:c.1762A>G

Protein change:

T588A

Links:

dbSNP: rs142846443

NCBI 1000 Genomes Browser:

rs142846443

Molecular consequence:

NM_000313.4:c.1762A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001314077.2:c.1858A>G - 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

Recent activity

Clear Turn Off Turn On

ATP-dependent RNA helicase DDX50 isoform X3 [Homo sapiens]
ATP-dependent RNA helicase DDX50 isoform X3 [Homo sapiens]
gi|2462520924|ref|XP_054222682.1|

Protein
proteasome subunit beta type-4 [Mus musculus]
proteasome subunit beta type-4 [Mus musculus]
gi|254540082|ref|NP_032971.2|

Protein
Mus musculus inhibitor of Bruton agammaglobulinemia tyrosine kinase (Ibtk), tran...
Mus musculus inhibitor of Bruton agammaglobulinemia tyrosine kinase (Ibtk), transcript variant 2, mRNA
gi|1327848486|ref|NM_175371.3|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000190487	CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation	no assertion criteria provided	Uncertain significance (Jun 1, 2014)	germline	research
SCV001306862	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24055113, 25637381 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000190487

CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation

no assertion criteria provided

Uncertain significance
(Jun 1, 2014)

germline

research

SCV001306862

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

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

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, research

Citations

PubMed

Actionable, pathogenic incidental findings in 1,000 participants' exomes.

Dorschner MO, Amendola LM, Turner EH, Robertson PD, Shirts BH, Gallego CJ, Bennett RL, Jones KL, Tokita MJ, Bennett JT, Kim JH, Rosenthal EA, Kim DS; National Heart, Lung, and Blood Institute Grand Opportunity Exome Sequencing Project., Tabor HK, Bamshad MJ, Motulsky AG, Scott CR, Pritchard CC, Walsh T, Burke W, Raskind WH, et al.

Am J Hum Genet. 2013 Oct 3;93(4):631-40. doi: 10.1016/j.ajhg.2013.08.006. Epub 2013 Sep 19.

PubMed [citation]

PMID:: 24055113
PMCID:: PMC3791261

Actionable exomic incidental findings in 6503 participants: challenges of variant classification.

Amendola LM, Dorschner MO, Robertson PD, Salama JS, Hart R, Shirts BH, Murray ML, Tokita MJ, Gallego CJ, Kim DS, Bennett JT, Crosslin DR, Ranchalis J, Jones KL, Rosenthal EA, Jarvik ER, Itsara A, Turner EH, Herman DS, Schleit J, Burt A, Jamal SM, et al.

Genome Res. 2015 Mar;25(3):305-15. doi: 10.1101/gr.183483.114. Epub 2015 Jan 30.

PubMed [citation]

PMID:: 25637381
PMCID:: PMC4352885

Details of each submission

From CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation, SCV000190487.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	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 Illumina Laboratory Services, Illumina, SCV001306862.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	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: Oct 13, 2024

ClinVar

Relating variation to medicine