NM_003289.4(TPM2):c.14AGA[2] (p.Lys7del) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 5, 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:: RCV000128675.6

Allele description [Variation Report for NM_003289.4(TPM2):c.14AGA[2] (p.Lys7del)]

NM_003289.4(TPM2):c.14AGA[2] (p.Lys7del)

Gene:

TPM2:tropomyosin 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

9p13.3

Genomic location:

Preferred name:

NM_003289.4(TPM2):c.14AGA[2] (p.Lys7del)

HGVS:

NC_000009.12:g.35689797CTT[2]
NG_011620.1:g.5254AGA[2]
NM_001301226.2:c.14AGA[2]
NM_001301227.2:c.14AGA[2]
NM_003289.4:c.14AGA[2]MANE SELECT
NM_213674.1:c.14AGA[2]
NP_001288155.1:p.Lys7del
NP_001288156.1:p.Lys7del
NP_003280.2:p.Lys7del
NP_998839.1:p.Lys7del
LRG_680t1:c.14AGA[2]
LRG_680:g.5254AGA[2]
LRG_680p1:p.Lys7del
NC_000009.11:g.35689793_35689795del
NC_000009.11:g.35689794CTT[2]
NM_003289.3:c.20_22delAGA
NM_003289.4:c.20_22delMANE SELECT
p.(Lys7del)

Protein change:

K7del

Links:

OMIM: 190990.0009; dbSNP: rs199476146

NCBI 1000 Genomes Browser:

rs199476146

Molecular consequence:

NM_001301226.2:c.14AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001301227.2:c.14AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_003289.4:c.14AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_213674.1:c.14AGA[2] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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putative N-acetylated-alpha-linked acidic dipeptidase isoform X1 [Macaca fascicu...
putative N-acetylated-alpha-linked acidic dipeptidase isoform X1 [Macaca fascicularis]
gi|544489023|ref|XP_005579379.1|

Protein
glycoside hydrolase N-terminal domain-containing protein [Capnocytophaga sp. ora...
glycoside hydrolase N-terminal domain-containing protein [Capnocytophaga sp. oral taxon 324]
gi|2786565825|ref|WP_369814597.1|

Protein
Bifidobacterium animalis strain 20224-6 chromosome, complete genome
Bifidobacterium animalis strain 20224-6 chromosome, complete genome
gi|2791970279|ref|NZ_CP139450.1|

Nucleotide
PREDICTED: Homo sapiens transcription factor 20 (TCF20), transcript variant X6, ...
PREDICTED: Homo sapiens transcription factor 20 (TCF20), transcript variant X6, mRNA
gi|2217340088|ref|XM_047441477.1|

Nucleotide
Homo sapiens chromosome 18, clone RP11-214L13, complete sequence
Homo sapiens chromosome 18, clone RP11-214L13, complete sequence
gi|16596606|gnl|WIBR|L9024|gb|AC027 |

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000172315	TPM2 homepage - Leiden Muscular Dystrophy pages	no classification provided	not provided	germline	not provided
SCV000709984	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 5, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000172315

TPM2 homepage - Leiden Muscular Dystrophy pages

no classification provided

not provided

germline

not provided

SCV000709984

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 5, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	1	not provided	literature only

Details of each submission

From TPM2 homepage - Leiden Muscular Dystrophy pages, SCV000172315.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV000709984.2

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

Description

Published functional studies support that c.20_22delAGA results in a protein with impaired localization, altered sarcomere structure, and impaired function (Mokbel et al., 2013; Davidson et al., 2013); In-frame deletion of 1 amino acids in a non-repeat region; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 26307083, 31060721, 23378224, 23413262, 22980765, 27726070, 25214167, 33060286, 35579956, 36233295)

#	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: Sep 29, 2024

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