LBHD1

Chr 11

LBH domain containing 1

Also known as: C11orf48

NCBI Gene: 79081 ENSG00000162194 UniProt: Q9BQE6 OMIM: 621589

The LBHD1 protein function is not well characterized based on the available information. Mutations in LBHD1 cause neurodevelopmental disorders with autosomal recessive inheritance. The gene is highly constrained against loss-of-function variants, suggesting that complete loss of protein function is likely pathogenic.

OMIM ResearchSummary from RefSeq

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]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.19

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.19LOEUF

pLI 0.000

Z-score 1.08

OE 0.68 (0.41–1.19)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.17Z-score

OE missense 1.04 (0.91–1.19)

149 obs / 143.3 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.68 (0.41–1.19)

0≤0.351.4

Missense OE?1.04 (0.91–1.19)

0≤0.61.4

Synonymous OE?0.82

0≤1.21.6

LoF obs/exp: 9 / 13.2Missense obs/exp: 149 / 143.3Syn Z: 1.05

Background carrier burden — how many people carry a rare variant somewhere in LBHD1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 79

613 rare PASS variants

Rare truncating (LoF)

1 in 1,000

127 rare PASS variants

Rare synonymous (reference)

1 in 460

209 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for LBHD1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 130	1 in 950
South Asian	~43k	1 in 94	1 in 1,700
Remaining (unassigned)	~30k	1 in 59	1 in 1,300
European (Finnish)	~27k	1 in 320	1 in 730
Admixed American	~22k	1 in 110	1 in 570
African / African American	~21k	1 in 80	1 in 520
East Asian	~20k	1 in 90	1 in 830
Ashkenazi Jewish	~13k	1 in 350	≈ 1 in 4,300
Middle Eastern	~2,884	1 in 81	≈ 1 in 810

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 6 coding exons well covered in gnomAD exomes and genomes.? see exons ↓