NM_007078.3(LDB3):c.1562A>G (p.Tyr521Cys) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Oct 17, 2016
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:: RCV000430714.1

Allele description [Variation Report for NM_007078.3(LDB3):c.1562A>G (p.Tyr521Cys)]

NM_007078.3(LDB3):c.1562A>G (p.Tyr521Cys)

Gene:

LDB3:LIM domain binding 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_007078.3(LDB3):c.1562A>G (p.Tyr521Cys)

HGVS:

NC_000010.11:g.86716657A>G
NG_008876.1:g.53094A>G
NM_001080114.2:c.1232A>G
NM_001171610.2:c.1577A>G
NM_001368064.1:c.1373A>G
NM_001368065.1:c.1373A>G
NM_001368066.1:c.1421A>G
NM_007078.3:c.1562A>GMANE SELECT
NP_001073583.1:p.Tyr411Cys
NP_001165081.1:p.Tyr526Cys
NP_001354993.1:p.Tyr458Cys
NP_001354994.1:p.Tyr458Cys
NP_001354995.1:p.Tyr474Cys
NP_009009.1:p.Tyr521Cys
LRG_385t1:c.1562A>G
LRG_385:g.53094A>G
NC_000010.10:g.88476414A>G
NM_007078.2:c.1562A>G

Protein change:

Y411C

Links:

dbSNP: rs535737552

NCBI 1000 Genomes Browser:

rs535737552

Molecular consequence:

NM_001080114.2:c.1232A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001171610.2:c.1577A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368064.1:c.1373A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368065.1:c.1373A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001368066.1:c.1421A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_007078.3:c.1562A>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000531973	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (Oct 17, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000531973

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely benign
(Oct 17, 2016)

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, SCV000531973.4

#	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

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