GeneBe

rs71019410

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_007078.3(LDB3):​c.896+6678_896+6697delCTCTCTCTCTCTCTCTCTCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000707 in 1,414,384 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 7.1e-7 ( 0 hom. )

Consequence

LDB3
NM_007078.3 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.30
Variant links:
Genes affected
LDB3 (HGNC:15710): (LIM domain binding 3) This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins involved in targeting and clustering of membrane proteins. The protein encoded by this gene interacts with alpha-actinin-2 through its N-terminal PDZ domain and with protein kinase C via its C-terminal LIM domains. The LIM domain is a cysteine-rich motif defined by 50-60 amino acids containing two zinc-binding modules. This protein also interacts with all three members of the myozenin family. Mutations in this gene have been associated with myofibrillar myopathy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding different isoforms have been identified; all isoforms have N-terminal PDZ domains while only longer isoforms (1, 2 and 5) have C-terminal LIM domains. [provided by RefSeq, Jan 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 10-86699239-TTCTCTCTCTCTCTCTCTCTC-T is Benign according to our data. Variant chr10-86699239-TTCTCTCTCTCTCTCTCTCTC-T is described in ClinVar as [Likely_benign]. Clinvar id is 2854959.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LDB3NM_007078.3 linkc.896+6678_896+6697delCTCTCTCTCTCTCTCTCTCT intron_variant Intron 7 of 13 ENST00000361373.9 NP_009009.1 O75112-1
LDB3NM_001368067.1 linkc.756-29_756-10delCTCTCTCTCTCTCTCTCTCT intron_variant Intron 8 of 8 ENST00000263066.11 NP_001354996.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LDB3ENST00000361373.9 linkc.896+6669_896+6688delTCTCTCTCTCTCTCTCTCTC intron_variant Intron 7 of 13 1 NM_007078.3 ENSP00000355296.3 O75112-1
LDB3ENST00000263066.11 linkc.756-38_756-19delTCTCTCTCTCTCTCTCTCTC intron_variant Intron 8 of 8 1 NM_001368067.1 ENSP00000263066.7 O75112-6
ENSG00000289258ENST00000443292.2 linkc.2406-38_2406-19delTCTCTCTCTCTCTCTCTCTC intron_variant Intron 17 of 17 1 ENSP00000393132.2 C9JWU6

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.07e-7
AC:
1
AN:
1414384
Hom.:
0
AF XY:
0.00000142
AC XY:
1
AN XY:
705990
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000256
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Myofibrillar myopathy 4 Benign:1
Apr 18, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-88458996; API