NM_007078.3(LDB3):c.295C>T (p.Pro99Ser) AND Cardiovascular phenotype

Germline classification:: Benign (1 submission)
Last evaluated:: Jan 24, 2022
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:: RCV002433677.2

Allele description [Variation Report for NM_007078.3(LDB3):c.295C>T (p.Pro99Ser)]

NM_007078.3(LDB3):c.295C>T (p.Pro99Ser)

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.295C>T (p.Pro99Ser)

HGVS:

NC_000010.11:g.86680131C>T
NG_008876.1:g.16568C>T
NM_001080114.2:c.295C>T
NM_001080115.2:c.295C>T
NM_001080116.1:c.295C>T
NM_001171610.2:c.295C>T
NM_001171611.2:c.295C>T
NM_001368063.1:c.295C>T
NM_001368064.1:c.295C>T
NM_001368065.1:c.295C>T
NM_001368066.1:c.295C>T
NM_001368067.1:c.295C>T
NM_001368068.1:c.295C>T
NM_007078.3:c.295C>TMANE SELECT
NP_001073583.1:p.Pro99Ser
NP_001073584.1:p.Pro99Ser
NP_001073585.1:p.Pro99Ser
NP_001165081.1:p.Pro99Ser
NP_001165082.1:p.Pro99Ser
NP_001354992.1:p.Pro99Ser
NP_001354993.1:p.Pro99Ser
NP_001354994.1:p.Pro99Ser
NP_001354995.1:p.Pro99Ser
NP_001354996.1:p.Pro99Ser
NP_001354997.1:p.Pro99Ser
NP_009009.1:p.Pro99Ser
LRG_385t1:c.295C>T
LRG_385t2:c.295C>T
LRG_385:g.16568C>T
LRG_385p2:p.Pro99Ser
NC_000010.10:g.88439888C>T
NM_007078.2:c.295C>T

Protein change:

P99S

Links:

dbSNP: rs201693259

NCBI 1000 Genomes Browser:

rs201693259

Molecular consequence:

NM_001080114.2:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001080115.2:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001080116.1:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001171610.2:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001171611.2:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368063.1:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368064.1:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368065.1:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368066.1:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368067.1:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368068.1:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_007078.3:c.295C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

Recent activity

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metal ABC transporter substrate-binding protein [Paraburkholderia acidiphila]
metal ABC transporter substrate-binding protein [Paraburkholderia acidiphila]
gi|1787164466|gnl|PRJNA534068|FAZ97 0|gb|QGZ58484.1|

Protein
LOC126743809 [Anthonomus grandis grandis]
LOC126743809 [Anthonomus grandis grandis]
Gene ID:126743809

Gene
LOC125436770 [Sphaerodactylus townsendi]
LOC125436770 [Sphaerodactylus townsendi]
Gene ID:125436770

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002751518	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Jan 24, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30775854, 30847666 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002751518

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Benign
(Jan 24, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Citations

PubMed

Genetic basis and outcome in a nationwide study of Finnish patients with hypertrophic cardiomyopathy.

Jääskeläinen P, Vangipurapu J, Raivo J, Kuulasmaa T, Heliö T, Aalto-Setälä K, Kaartinen M, Ilveskoski E, Vanninen S, Hämäläinen L, Melin J, Kokkonen J, Nieminen MS; FinHCM Study Group., Laakso M, Kuusisto J.

ESC Heart Fail. 2019 Apr;6(2):436-445. doi: 10.1002/ehf2.12420. Epub 2019 Feb 18.

PubMed [citation]

PMID:: 30775854
PMCID:: PMC6437444

Large next-generation sequencing gene panels in genetic heart disease: yield of pathogenic variants and variants of unknown significance.

van Lint FHM, Mook ORF, Alders M, Bikker H, Lekanne Dit Deprez RH, Christiaans I.

Neth Heart J. 2019 Jun;27(6):304-309. doi: 10.1007/s12471-019-1250-5.

PubMed [citation]

PMID:: 30847666
PMCID:: PMC6533346

Details of each submission

From Ambry Genetics, SCV002751518.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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: Sep 29, 2024

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