NM_001018005.2(TPM1):c.310G>C (p.Glu104Gln) AND Hypertrophic cardiomyopathy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 11, 2020
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:: RCV001860570.5

Allele description [Variation Report for NM_001018005.2(TPM1):c.310G>C (p.Glu104Gln)]

NM_001018005.2(TPM1):c.310G>C (p.Glu104Gln)

Gene:

TPM1:tropomyosin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q22.2

Genomic location:

Preferred name:

NM_001018005.2(TPM1):c.310G>C (p.Glu104Gln)

HGVS:

NC_000015.10:g.63057054G>C
NG_007557.1:g.19416G>C
NM_000366.6:c.310G>C
NM_001018004.2:c.310G>C
NM_001018005.2:c.310G>CMANE SELECT
NM_001018006.2:c.310G>C
NM_001018007.2:c.310G>C
NM_001018008.2:c.202G>C
NM_001018020.2:c.310G>C
NM_001301244.2:c.310G>C
NM_001301289.2:c.202G>C
NM_001330344.2:c.202G>C
NM_001330346.2:c.202G>C
NM_001330351.2:c.202G>C
NM_001365776.1:c.310G>C
NM_001365777.1:c.310G>C
NM_001365778.1:c.436G>C
NM_001365779.1:c.310G>C
NM_001365780.1:c.202G>C
NM_001365781.2:c.202G>C
NM_001365782.1:c.202G>C
NP_000357.3:p.Glu104Gln
NP_001018004.1:p.Glu104Gln
NP_001018005.1:p.Glu104Gln
NP_001018006.1:p.Glu104Gln
NP_001018007.1:p.Glu104Gln
NP_001018008.1:p.Glu68Gln
NP_001018020.1:p.Glu104Gln
NP_001288173.1:p.Glu104Gln
NP_001288218.1:p.Glu68Gln
NP_001317273.1:p.Glu68Gln
NP_001317275.1:p.Glu68Gln
NP_001317280.1:p.Glu68Gln
NP_001352705.1:p.Glu104Gln
NP_001352706.1:p.Glu104Gln
NP_001352707.1:p.Glu146Gln
NP_001352708.1:p.Glu104Gln
NP_001352709.1:p.Glu68Gln
NP_001352710.1:p.Glu68Gln
NP_001352711.1:p.Glu68Gln
LRG_387t1:c.310G>C
LRG_387:g.19416G>C
LRG_387p1:p.Glu104Gln
NC_000015.9:g.63349253G>C
NC_000015.9:g.63349253G>C
p.Glu104Gln

Protein change:

E104Q

Links:

dbSNP: rs1596361132

NCBI 1000 Genomes Browser:

rs1596361132

Molecular consequence:

NM_000366.6:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001018004.2:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001018005.2:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001018006.2:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001018007.2:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001018008.2:c.202G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001018020.2:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001301244.2:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001301289.2:c.202G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001330344.2:c.202G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001330346.2:c.202G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001330351.2:c.202G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001365776.1:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001365777.1:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001365778.1:c.436G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001365779.1:c.310G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001365780.1:c.202G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001365781.2:c.202G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001365782.1:c.202G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hypertrophic cardiomyopathy
Synonyms:: HYPERTROPHIC MYOCARDIOPATHY
Identifiers:: MONDO: MONDO:0005045; MeSH: D002312; MedGen: C0007194; Human Phenotype Ontology: HP:0001639

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002125514	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 11, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002125514

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 11, 2020)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002125514.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with TPM1-related conditions. ClinVar contains an entry for this variant (Variation ID: 813935). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with glutamine at codon 104 of the TPM1 protein (p.Glu104Gln). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and glutamine.

#	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: Mar 30, 2024

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