NM_005422.4(TECTA):c.3012C>G (p.Thr1004=) AND not specified

Germline classification:: Benign (2 submissions)
Last evaluated:: Nov 6, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000038490.15

Allele description [Variation Report for NM_005422.4(TECTA):c.3012C>G (p.Thr1004=)]

NM_005422.4(TECTA):c.3012C>G (p.Thr1004=)

Genes:

TBCEL-TECTA:TBCEL-TECTA readthrough [Gene - HGNC]
TECTA:tectorin alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_005422.4(TECTA):c.3012C>G (p.Thr1004=)

HGVS:

NC_000011.10:g.121137491C>G
NG_011633.1:g.39826C>G
NM_001378761.1:c.3969C>G
NM_005422.4:c.3012C>GMANE SELECT
NP_001365690.1:p.Thr1323=
NP_005413.2:p.Thr1004=
NP_005413.2:p.Thr1004=
NC_000011.9:g.121008200C>G
NM_005422.2:c.3012C>G
c.3012C>G
p.Thr1004Thr

Links:

dbSNP: rs61291716

NCBI 1000 Genomes Browser:

rs61291716

Molecular consequence:

NM_001378761.1:c.3969C>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_005422.4:c.3012C>G - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

Clear Turn Off Turn On

PREDICTED: Rattus norvegicus radical S-adenosyl methionine domain containing 2 (...
PREDICTED: Rattus norvegicus radical S-adenosyl methionine domain containing 2 (Rsad2), transcript variant X1, mRNA
gi|2678953226|ref|XM_039112917.2|

Nucleotide
OSLEUM clade 18S ribosomal RNA gene, partial sequence; internal transcribed spac...
OSLEUM clade 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence.
PopSet: 1280049738

PopSet
Homo sapiens clathrin, heavy chain-like 1, mRNA (cDNA clone IMAGE:40021667), par...
Homo sapiens clathrin, heavy chain-like 1, mRNA (cDNA clone IMAGE:40021667), partial cds
gi|133777367|gb|BC113030.1|

Nucleotide
Rhinolophus sinicus isolate:Zhonghua_01
Rhinolophus sinicus isolate:Zhonghua_01
Rhinolophus sinicus isolate:Zhonghua_01 RefSeq Genome sequencing and assembly

BioProject
BioProject Links for Nucleotide (Select 1124039786) (1)
BioProject

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000062168	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Apr 30, 2012)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000718770	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Nov 6, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000062168

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Apr 30, 2012)

germline

clinical testing

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

SCV000718770

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Nov 6, 2017)

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	not provided	24	24	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000062168.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	24	not provided	not provided	clinical testing	PubMed (1)

Description

Thr1004Thr in Exon 10 of TECTA: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 7.0% (261/3738) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs61291716).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		24	not provided	24	not provided

From GeneDx, SCV000718770.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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

ClinVar

Relating variation to medicine