NM_012470.4(TNPO3):c.140C>G (p.Ser47Ter) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 19, 2023
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:: RCV003317903.1

Allele description [Variation Report for NM_012470.4(TNPO3):c.140C>G (p.Ser47Ter)]

NM_012470.4(TNPO3):c.140C>G (p.Ser47Ter)

Gene:

TNPO3:transportin 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q32.1

Genomic location:

Preferred name:

NM_012470.4(TNPO3):c.140C>G (p.Ser47Ter)

HGVS:

NC_000007.14:g.129018138G>C
NG_023428.1:g.42036C>G
NM_001191028.3:c.140C>G
NM_001382216.1:c.140C>G
NM_001382217.1:c.140C>G
NM_001382218.1:c.140C>G
NM_001382219.1:c.140C>G
NM_001382220.1:c.140C>G
NM_001382221.1:c.140C>G
NM_001382222.1:c.140C>G
NM_001382223.1:c.140C>G
NM_012470.4:c.140C>GMANE SELECT
NP_001177957.2:p.Ser47Ter
NP_001369145.1:p.Ser47Ter
NP_001369146.1:p.Ser47Ter
NP_001369147.1:p.Ser47Ter
NP_001369148.1:p.Ser47Ter
NP_001369149.1:p.Ser47Ter
NP_001369150.1:p.Ser47Ter
NP_001369151.1:p.Ser47Ter
NP_001369152.1:p.Ser47Ter
NP_036602.1:p.Ser47Ter
NC_000007.13:g.128658192G>C
NM_012470.3:c.140C>G
NR_034053.3:n.642C>G
NR_167911.1:n.606C>G
NR_167912.1:n.481C>G
NR_167913.1:n.481C>G
NR_167914.1:n.481C>G
NR_167915.1:n.642C>G
NR_167916.1:n.481C>G
NR_167917.1:n.481C>G
NR_167918.1:n.767C>G
NR_167919.1:n.606C>G
NR_167920.1:n.767C>G
NR_167921.1:n.606C>G
NR_167922.1:n.481C>G
NR_167923.1:n.606C>G
NR_167924.1:n.481C>G
NR_167925.1:n.481C>G
NR_167926.1:n.642C>G
NR_167927.1:n.606C>G

Protein change:

S47*

Molecular consequence:

NR_034053.3:n.642C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167911.1:n.606C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167912.1:n.481C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167913.1:n.481C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167914.1:n.481C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167915.1:n.642C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167916.1:n.481C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167917.1:n.481C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167918.1:n.767C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167919.1:n.606C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167920.1:n.767C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167921.1:n.606C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167922.1:n.481C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167923.1:n.606C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167924.1:n.481C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167925.1:n.481C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167926.1:n.642C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_167927.1:n.606C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001191028.3:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001382216.1:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001382217.1:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001382218.1:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001382219.1:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001382220.1:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001382221.1:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001382222.1:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001382223.1:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_012470.4:c.140C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004021092	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jun 19, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004021092

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jun 19, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004021092.1

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

Description

Variant summary: TNPO3 c.140C>G (p.Ser47X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay. However, current evidence do not allow for conclusions whether LoF variants in TNPO3 gene cause disease. The variant was absent in 251228 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.140C>G in individuals affected with Autosomal Dominant Limb-Girdle Muscular Dystrophy Type 1F and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: Jul 29, 2023

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