NM_005902.4(SMAD3):c.5C>A (p.Ser2Ter) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 4, 2018
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:: RCV000521242.1

Allele description [Variation Report for NM_005902.4(SMAD3):c.5C>A (p.Ser2Ter)]

NM_005902.4(SMAD3):c.5C>A (p.Ser2Ter)

Genes:

LOC130057352:ATAC-STARR-seq lymphoblastoid silent region 6574 [Gene]
SMAD3:SMAD family member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q22.33

Genomic location:

Preferred name:

NM_005902.4(SMAD3):c.5C>A (p.Ser2Ter)

HGVS:

NC_000015.10:g.67066159C>A
NG_011990.1:g.5303C>A
NM_005902.4:c.5C>AMANE SELECT
NP_005893.1:p.Ser2Ter
NC_000015.9:g.67358497C>A
NM_005902.3:c.5C>A

Protein change:

S2*

Links:

dbSNP: rs1006530719

NCBI 1000 Genomes Browser:

rs1006530719

Molecular consequence:

NM_005902.4:c.5C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000620422	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Apr 4, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000620422

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Apr 4, 2018)

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, SCV000620422.1

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

Description

The S2X likely pathogenic variant in the SMAD3 gene has not been published as pathogenic or been reported as benign to our knowledge. S2X is predicted to cause loss of normal protein function either by protein truncation or nonsense-mediated mRNA decay. Other nonsense variants in the SMAD3 gene have been reported in Human Gene Mutation Database in association with LDS3 (Stenson et al., 2014). Furthermore, the S2X variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server).

#	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: Feb 28, 2024

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