LDB2

LIM domain binding 2, the group of Wnt enhanceosome complex

Basic information

Region (hg38): 4:16501540-16898678

Links

ENSG00000169744 ∙ NCBI:9079 ∙ OMIM:603450 ∙ HGNC:6533 ∙ Uniprot:O43679 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LDB2 gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDB2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in LDB2

This is a list of pathogenic ClinVar variants found in the LDB2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-16502759-C-T		not specified	Uncertain significance (Nov 07, 2023)
4-16502764-A-C		not specified	Uncertain significance (May 30, 2023)
4-16502776-G-T		not specified	Uncertain significance (Dec 05, 2022)
4-16511990-C-A		not specified	Uncertain significance (Jan 18, 2022)
4-16512098-C-T		not specified	Uncertain significance (Dec 03, 2021)
4-16588771-G-A		not specified	Uncertain significance (Oct 13, 2023)
4-16595714-T-C		not specified	Uncertain significance (Dec 15, 2022)
4-16595821-A-G		not specified	Uncertain significance (Sep 30, 2021)
4-16759189-T-C			Benign (May 03, 2018)
4-16898413-T-C		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDB2	protein_coding	protein_coding	ENST00000304523	8	397269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.955	0.0454	125731	0	3	125734	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.37	118	216	0.546	0.0000116	2479
Missense in Polyphen		34	77.394	0.43931		872
Synonymous	0.317	82	85.7	0.956	0.00000573	686
Loss of Function	3.56	2	18.5	0.108	8.75e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000943	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000367	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the LIM domain of a wide variety of LIM domain- containing transcription factors.
• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.0432
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.928
• hipred: Y
• hipred_score: 0.825
• ghis: 0.667

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ldb2
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: ldb2a
• Affected structure: nodal signaling pathway
• Phenotype tag: abnormal
• Phenotype quality: increased process quality

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;hair follicle development;multicellular organism development;epithelial structure maintenance;regulation of cell migration;somatic stem cell population maintenance;regulation of kinase activity;positive regulation of cellular component biogenesis;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;transcription factor complex;nucleolus;plasma membrane;cell leading edge
• Molecular function: RNA polymerase II activating transcription factor binding;transcription coregulator activity;protein binding;enzyme binding;LIM domain binding