NM_006280.3(SSR4):c.184C>T (p.Gln62Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 27, 2021
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:: RCV001994695.4

Allele description [Variation Report for NM_006280.3(SSR4):c.184C>T (p.Gln62Ter)]

NM_006280.3(SSR4):c.184C>T (p.Gln62Ter)

Gene:

SSR4:signal sequence receptor subunit 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_006280.3(SSR4):c.184C>T (p.Gln62Ter)

HGVS:

NC_000023.11:g.153796550C>T
NG_041795.1:g.7376C>T
NM_001204526.1:c.217C>T
NM_001204527.2:c.208C>T
NM_006280.3:c.184C>TMANE SELECT
NP_001191455.1:p.Gln73Ter
NP_001191456.1:p.Gln70Ter
NP_006271.1:p.Gln62Ter
NC_000023.10:g.153062005C>T
NR_037927.1:n.529C>T

Protein change:

Q62*

Links:

dbSNP: rs868996072

NCBI 1000 Genomes Browser:

rs868996072

Molecular consequence:

NR_037927.1:n.529C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001204526.1:c.217C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001204527.2:c.208C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_006280.3:c.184C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Homo sapiens nucleolar protein 8 (NOL8), transcript variant X3, mRNA
PREDICTED: Homo sapiens nucleolar protein 8 (NOL8), transcript variant X3, mRNA
gi|2462625201|ref|XM_054363206.1|

Nucleotide
Homo sapiens catenin alpha 3 (CTNNA3), RefSeqGene on chromosome 10
Homo sapiens catenin alpha 3 (CTNNA3), RefSeqGene on chromosome 10
gi|2310185047|ref|NG_034072.2|

Nucleotide
protein kinase [Achlya hypogyna]
protein kinase [Achlya hypogyna]
gi|1173944398|gb|OQR93140.1||gnl|WG R|ACHHYP_02855.1

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002229986	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 27, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24218363, 26264460, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002229986

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 27, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Citations

PubMed

A new congenital disorder of glycosylation caused by a mutation in SSR4, the signal sequence receptor 4 protein of the TRAP complex.

Losfeld ME, Ng BG, Kircher M, Buckingham KJ, Turner EH, Eroshkin A, Smith JD, Shendure J, Nickerson DA, Bamshad MJ; University of Washington Center for Mendelian Genomics., Freeze HH.

Hum Mol Genet. 2014 Mar 15;23(6):1602-5. doi: 10.1093/hmg/ddt550. Epub 2013 Nov 11.

PubMed [citation]

PMID:: 24218363
PMCID:: PMC3929095

Expanding the Molecular and Clinical Phenotype of SSR4-CDG.

Ng BG, Raymond K, Kircher M, Buckingham KJ, Wood T, Shendure J, Nickerson DA, Bamshad MJ; University of Washington Center for Mendelian Genomics., Wong JT, Monteiro FP, Graham BH, Jackson S, Sparkes R, Scheuerle AE, Cathey S, Kok F, Gibson JB, Freeze HH.

Hum Mutat. 2015 Nov;36(11):1048-51. doi: 10.1002/humu.22856. Epub 2015 Aug 27.

PubMed [citation]

PMID:: 26264460
PMCID:: PMC4604052

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002229986.3

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with SSR4-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gln73*) in the SSR4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SSR4 are known to be pathogenic (PMID: 24218363, 26264460).

#	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: Sep 29, 2024

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