NM_013296.5(GPSM2):c.1569TTC[1] (p.Ser525del) AND not specified

Germline classification:: Benign (2 submissions)
Last evaluated:: Oct 31, 2014
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000218159.9

Allele description [Variation Report for NM_013296.5(GPSM2):c.1569TTC[1] (p.Ser525del)]

NM_013296.5(GPSM2):c.1569TTC[1] (p.Ser525del)

Gene:

GPSM2:G protein signaling modulator 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

1p13.3

Genomic location:

Preferred name:

NM_013296.5(GPSM2):c.1569TTC[1] (p.Ser525del)

HGVS:

NC_000001.10:g.109465166_109465168del
NC_000001.11:g.108922545TTC[1]
NG_028108.2:g.52196TTC[1]
NM_001321038.2:c.1569TTC[1]
NM_001321039.3:c.1569TTC[1]
NM_013296.5:c.1569TTC[1]MANE SELECT
NP_001307967.1:p.Ser525del
NP_001307968.1:p.Ser525del
NP_037428.3:p.Ser525del
LRG_1373t1:c.1569TTC[1]
LRG_1373:g.52196TTC[1]
LRG_1373p1:p.Ser525del
NC_000001.10:g.109465166_109465168del
NC_000001.10:g.109465167TTC[1]
NC_000001.10:g.109465170_109465172delTTC
NM_013296.4:c.1572_1574del
NM_013296.4:c.1572_1574delTTC

Protein change:

S525del

Links:

dbSNP: rs35029887

NCBI 1000 Genomes Browser:

rs35029887

Molecular consequence:

NM_001321038.2:c.1569TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001321039.3:c.1569TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_013296.5:c.1569TTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Observations:

511

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000269139	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Oct 31, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000311961	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	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

SCV000269139

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Oct 31, 2014)

germline

clinical testing

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

SCV000311961

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

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	not provided	516	511	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

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 Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000269139.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	516	not provided	not provided	clinical testing	PubMed (1)

Description

Ser525del in exon 13 of GPSM2: This variant is a deletion of 1 amino acid at pos ition 525 and is not predicted to alter the protein reading-frame or impact the protein. It has been identified in in 28% (2331/8254) of European American chrom osomes and 56% (2409/4266) of African American chromosomes by the NHLBI Exome Se quencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs35029887).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		516	not provided	511	not provided

From PreventionGenetics, part of Exact Sciences, SCV000311961.1

#	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: Oct 26, 2024

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