NM_006306.4(SMC1A):c.796AAG[2] (p.Lys268del) AND SMC1A-related disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 22, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV004730888.1

Allele description [Variation Report for NM_006306.4(SMC1A):c.796AAG[2] (p.Lys268del)]

NM_006306.4(SMC1A):c.796AAG[2] (p.Lys268del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

Xp11.22

Genomic location:

Preferred name:

NM_006306.4(SMC1A):c.796AAG[2] (p.Lys268del)

HGVS:

NC_000023.11:g.53412952TCT[2]
NG_006988.2:g.14713AAG[2]
NM_001281463.1:c.730AAG[2]
NM_006306.4:c.796AAG[2]MANE SELECT
NM_006306.4:c.802_804del
NP_001268392.1:p.Lys246del
NP_006297.2:p.Lys268del
LRG_773t1:c.730AAG[2]
LRG_773:g.14713AAG[2]
LRG_773p1:p.Lys246del
NC_000023.10:g.53439902TCT[2]
NM_006306.2:c.802_804del
NM_006306.3:c.802_804delAAG
NM_006306.4:c.802_804delMANE SELECT
NM_006306.4:c.802_804delAAGMANE SELECT
c.802_804del(p.K268del)

Protein change:

K246del

Links:

dbSNP: rs727503773

NCBI 1000 Genomes Browser:

rs727503773

Molecular consequence:

NM_001281463.1:c.730AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_006306.4:c.796AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: SMC1A-related disorder
Synonyms:: SMC1A-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005339606	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Pathogenic (Jul 22, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005339606

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Pathogenic
(Jul 22, 2024)

germline

clinical testing

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005339606.1

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

Description

The SMC1A c.802_804delAAG variant is predicted to result in an in-frame deletion (p.Lys268del). This variant has been reported as a recurrent de novo variant in individuals with Cornelia de Lange syndrome (Liu et al. 2009. PubMed ID: 19701948; Yuan et al. 2019. PubMed ID: 30158690; Stojanovic et al. 2019. PubMed ID: 31623504; Table S1, Pode-Shakked et al. 2021. PubMed ID: 34580403; Kaur et al. 2023. PubMed ID: 37377026). This variant has not been reported in the gnomAD database, indicating this variant is rare. This variant is interpreted as pathogenic.

#	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 8, 2024

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