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

Germline classification:: Benign (3 submissions)
Last evaluated:: Feb 1, 2024
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:: RCV000711834.11

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]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

PREDICTED: Gossypium hirsutum disease resistance protein RPS2 (LOC107951782), tr...
PREDICTED: Gossypium hirsutum disease resistance protein RPS2 (LOC107951782), transcript variant X2, mRNA
gi|2029638806|ref|XM_016886918.2|

Nucleotide
Duchenne Muscular Dystrophy response to oxandrolone (HG-U133A)
Duchenne Muscular Dystrophy response to oxandrolone (HG-U133A)
Accession: GDS1333

GEO DataSets
Related DataSets for GEO Profiles (Select 12583784) (1)
GEO DataSets

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
SCV000842239	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (May 9, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001828599	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Jan 14, 2016)	germline	clinical testing	Citation Link,
SCV002403180	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	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

SCV000842239

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(May 9, 2018)

germline

clinical testing

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

SCV001828599

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Jan 14, 2016)

germline

clinical testing

Citation Link,

SCV002403180

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Feb 1, 2024)

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	yes	not provided	not provided	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 Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Athena Diagnostics, SCV000842239.1

#	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

From GeneDx, SCV001828599.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002403180.3

#	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

ClinVar

Relating variation to medicine