NM_013296.5(GPSM2):c.1501del (p.Ser501fs) AND Chudley-McCullough syndrome

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Nov 3, 2021
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:: RCV001072143.3

Allele description [Variation Report for NM_013296.5(GPSM2):c.1501del (p.Ser501fs)]

NM_013296.5(GPSM2):c.1501del (p.Ser501fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1p13.3

Genomic location:

Preferred name:

NM_013296.5(GPSM2):c.1501del (p.Ser501fs)

HGVS:

NC_000001.11:g.108922477del
NG_028108.2:g.52128del
NM_001321038.2:c.1501del
NM_001321039.3:c.1501del
NM_013296.5:c.1501delMANE SELECT
NP_001307967.1:p.Ser501fs
NP_001307968.1:p.Ser501fs
NP_037428.3:p.Ser501fs
LRG_1373t1:c.1501del
LRG_1373:g.52128del
LRG_1373p1:p.Ser501fs
NC_000001.10:g.109465099del
NM_013296.5:c.1501delAMANE SELECT

Protein change:

S501fs

Links:

dbSNP: rs761092578

NCBI 1000 Genomes Browser:

rs761092578

Molecular consequence:

NM_001321038.2:c.1501del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001321039.3:c.1501del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_013296.5:c.1501del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Chudley-McCullough syndrome (CMCS)
Synonyms:: Deafness, sensorineural, with partial agenesis of the corpus callosum and arachnoid cysts; Deafness, bilateral sensorineural, and hydrocephalus due to foramen of monro obstruction; Deafness, autosomal recessive 82
Identifiers:: MONDO: MONDO:0011411; MedGen: C1858695; Orphanet: 314597; OMIM: 604213

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001235709	Bruce Lefroy Centre, Murdoch Childrens Research Institute	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 1, 2020)	inherited	research	PubMed (1) [See all records that cite this PMID]
SCV002788122	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 3, 2021)	unknown	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

SCV001235709

Bruce Lefroy Centre, Murdoch Childrens Research Institute

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 1, 2020)

inherited

research

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

SCV002788122

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 3, 2021)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	inherited	yes	3	1	not provided	not provided	yes	research

Citations

PubMed

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 Bruce Lefroy Centre, Murdoch Childrens Research Institute, SCV001235709.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	yes	research	PubMed (1)

Description

Affected individual is homozygous for this variant. Both parents are heterozygotes and clinically unnaffected.

Description

PM2, PM3, PM4, PP3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	not provided	not provided	not provided		3	not provided	1	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002788122.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jan 7, 2023

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