LBHD1

protein-coding

LBH domain containing 1

Gene summary

This gene shares three exons in common with another gene, chromosome 11 open reading frame 98 (GeneID:102288414), but the encoded protein uses a reading frame that is different from that of the chromosome 11 open reading frame 98 gene. [provided by RefSeq, Nov 2017]

Previous symbols:

C11orf48

MANE transcript

NM_024099.5

Inheritance

—

ClinVar variants

U:51B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr11:62,662,817-62,672,267

External References & Databases

Ensembl (ENSG00000162194)

Transcript & Mutation Effects

hg38 • Region Span ~9.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LBHD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 90

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024099.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			48 clinvar	2 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	51	2	0	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024099.5	RefSeq	NP_077004.2	6	MANE Select
ENST00000354588.8	Ensembl	ENSP00000346600.3	6	MANE Select
NM_001367940.2	RefSeq	NP_001354869.1	5	Standard
NM_001367941.2	RefSeq	NP_001354870.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000532208
Coding exons: 6
Length: 9441
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125747
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.168	149	143	1.04	0.00000679	1730
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.59
RVIS percentile EVS: 82.51

Essentials

Essential (gene trap): N