NM_006306.4(SMC1A):c.3268C>T (p.Arg1090Cys) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 7, 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:: RCV001794795.2

Allele description [Variation Report for NM_006306.4(SMC1A):c.3268C>T (p.Arg1090Cys)]

NM_006306.4(SMC1A):c.3268C>T (p.Arg1090Cys)

Gene:

SMC1A:structural maintenance of chromosomes 1A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.22

Genomic location:

Preferred name:

NM_006306.4(SMC1A):c.3268C>T (p.Arg1090Cys)

HGVS:

NC_000023.11:g.53382523G>A
NG_006988.2:g.45148C>T
NM_001281463.1:c.3202C>T
NM_006306.4:c.3268C>TMANE SELECT
NP_001268392.1:p.Arg1068Cys
NP_006297.2:p.Arg1090Cys
LRG_773t1:c.3202C>T
LRG_773:g.45148C>T
LRG_773p1:p.Arg1068Cys
NC_000023.10:g.53409444G>A
NM_006306.2:c.3268C>T

Protein change:

R1068C

Links:

dbSNP: rs2146582558

NCBI 1000 Genomes Browser:

rs2146582558

Molecular consequence:

NM_001281463.1:c.3202C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006306.4:c.3268C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Mus musculus collagen, type VIII, alpha 2 (Col8a2), mRNA
Mus musculus collagen, type VIII, alpha 2 (Col8a2), mRNA
gi|118130942|ref|NM_199473.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002032770	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Dec 7, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002032770

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Dec 7, 2021)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV002032770.2

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

Description

Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (Lek et al., 2016); Missense variants in this gene are often considered pathogenic (Stenson et al., 2014); This variant is associated with the following publications: (PMID: 28607419)

#	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

Last Updated: Dec 24, 2023

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