LBH

LBH regulator of WNT signaling pathway

Basic information

Region (hg38): 2:30231534-30323730

Links

ENSG00000213626 ∙ NCBI:81606 ∙ OMIM:611763 ∙ HGNC:29532 ∙ Uniprot:Q53QV2 ∙ 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 LBH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LBH 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	1	0

Variants in LBH

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

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

Position	Type	Phenotype	Significance	ClinVar
2-30234411-C-A		not specified	Uncertain significance (Dec 05, 2022)
2-30234443-T-A		not specified	Uncertain significance (May 01, 2024)
2-30234480-C-A		not specified	Uncertain significance (Jan 03, 2022)
2-30257481-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-30257538-C-T		not specified	Uncertain significance (Apr 08, 2024)
2-30257572-A-G		not specified	Uncertain significance (Jan 30, 2024)
2-30257587-G-A		not specified	Uncertain significance (Oct 27, 2023)
2-30257599-C-T		not specified	Uncertain significance (Mar 23, 2023)
2-30257600-G-A		not specified	Likely benign (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LBH	protein_coding	protein_coding	ENST00000395323	3	92200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0144	0.696	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.591	53	66.6	0.796	0.00000400	699
Missense in Polyphen		18	32.9	0.54711		311
Synonymous	-0.316	27	25.0	1.08	0.00000156	184
Loss of Function	0.619	3	4.40	0.682	1.86e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000367	0.0000352
Middle Eastern	0.000326	0.000326
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator which may act in mitogen- activated protein kinase signaling pathway. {ECO:0000269|PubMed:17390236}.

Intolerance Scores

• loftool: 0.305
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.411
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lbh
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; reproductive system phenotype; normal phenotype

Zebrafish Information Network

• Gene name: lbh
• Affected structure: ceratobranchial cartilage
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: negative regulation of intracellular estrogen receptor signaling pathway;positive regulation of transcription, DNA-templated;mammary gland epithelial cell differentiation;positive regulation of somatic stem cell population maintenance;positive regulation of somatic stem cell division;positive regulation of mammary stem cell proliferation;negative regulation of stem cell differentiation
• Cellular component: nucleus;cytoplasm