LBHD1

LBH domain containing 1

Basic information

Region (hg38): 11:62662817-62672267

Previous symbols: [ "C11orf48" ]

Links

ENSG00000162194 ∙ NCBI:79081 ∙ ∙ HGNC:28351 ∙ Uniprot:Q9BQE6 ∙ 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 LBHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LBHD1 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						0
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			26	10	6	42
Total	0	0	36	11	6

Variants in LBHD1

This is a list of pathogenic ClinVar variants found in the LBHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62663240-C-T		not specified	Uncertain significance (Mar 01, 2023)
11-62663244-G-C		not specified	Uncertain significance (Jun 06, 2023)
11-62664937-A-C		not specified	Uncertain significance (Mar 21, 2024)
11-62664970-G-A		not specified	Uncertain significance (Mar 29, 2024)
11-62666419-G-A		not specified	Uncertain significance (Jan 29, 2024)
11-62666509-C-T			Benign (Jan 12, 2018)
11-62666512-G-C		not specified	Uncertain significance (Jun 16, 2024)
11-62666557-C-G		not specified	Uncertain significance (May 20, 2024)
11-62666561-G-C		not specified	Uncertain significance (Aug 17, 2022)
11-62666576-G-C		not specified	Uncertain significance (Aug 04, 2021)
11-62666596-T-C		not specified	Uncertain significance (Dec 11, 2023)
11-62666675-T-G		not specified	Uncertain significance (Jun 24, 2022)
11-62666681-G-T		not specified	Uncertain significance (Dec 14, 2023)
11-62666726-A-G		not specified	Uncertain significance (Jan 24, 2024)
11-62666839-C-T		not specified	Uncertain significance (Nov 06, 2023)
11-62666840-G-C		not specified	Uncertain significance (Jan 17, 2024)
11-62666884-A-G		not specified	Uncertain significance (Jun 06, 2023)
11-62666978-C-G		not specified	Uncertain significance (Sep 13, 2023)
11-62666998-G-C		not specified	Uncertain significance (Jun 10, 2024)
11-62667002-C-T		not specified	Uncertain significance (May 25, 2022)
11-62667670-C-T		not specified	Uncertain significance (Jul 19, 2023)
11-62667671-C-G		not specified	Uncertain significance (Feb 22, 2023)
11-62667690-A-T		not specified	Uncertain significance (May 06, 2024)
11-62667715-G-C		not specified	Uncertain significance (Jan 24, 2023)
11-62667727-C-A		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LBHD1	protein_coding	protein_coding	ENST00000532208	6	9441

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000206	0.730	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.168	149	143	1.04	0.00000679	1730
Missense in Polyphen		38	40.306	0.94279		421
Synonymous	1.05	45	54.9	0.820	0.00000292	493
Loss of Function	1.08	9	13.2	0.680	5.73e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.000598	0.000598
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.51

Haploinsufficiency Scores

• pHI: 0.0600
• hipred: N
• hipred_score: 0.123
• ghis: 0.391

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Lbhd1