LDB1

protein-coding

LIM domain binding 1, the group of Wnt enhanceosome complex

Gene summary

Enables LIM domain binding activity; RNA polymerase II-specific DNA-binding transcription factor binding activity; and enzyme binding activity. Involved in negative regulation of DNA-templated transcription and positive regulation of transcription by RNA polymerase II. Located in chromatin. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001113407.3

Inheritance

ClinVar variants

P:13U:38B:2

Top phenotype

congenital hydrocephalus

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr10:102,106,489-102,120,368

External References & Databases

Ensembl (ENSG00000198728)

Transcript & Mutation Effects

hg38 • Region Span ~13.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

congenital hydrocephalusSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0016349

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LDB1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 26

not providedTotal: 15

Autosomal dominant non-syndromic intellectual disabilityTotal: 13

LDB1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001113407.3. 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				1 clinvar		1
missense		3 clinvar	32 clinvar	1 clinvar		36
nonsense	3 clinvar	1 clinvar	2 clinvar			6
start loss						0
frameshift	4 clinvar		4 clinvar			8
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar				2
Total	8	5	38	2	0	53

Highest pathogenic variant AF is 6.851305e-7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001113407.3	RefSeq	NP_001106878.1	11	MANE Select
ENST00000673968.1	Ensembl	ENSP00000501277.1	11	MANE Select
NM_001321612.2	RefSeq	NP_001308541.1	11	Standard
NM_003893.5	RefSeq	NP_003884.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transcriptional misregulation in cancer - Homo sapiens (human)
Developmental Biology
Gene expression (Transcription)
multi-step regulation of transcription by pitx2
Generic Transcription Pathway

Biological Process

negative regulation of transcription by RNA polymerase II
transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery
gastrulation with mouth forming second
hair follicle development
transcription, DNA-templated

Molecular Function

RNA polymerase II activating transcription factor binding
enhancer sequence-specific DNA binding
chromatin binding
transcription corepressor activity
protein binding

Cellular Component

nuclear chromatin
nucleus
nucleoplasm
transcription factor complex
cell leading edge

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000425280
Coding exons: 11
Length: 12894
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125744
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.81	132	259	0.509	0.0000161	2741
Missense (PolyPhen)		40	112.95	0.35415		1113
Synonymous	0.0546	98	98.7	0.993	0.00000663	745
Loss of Function	3.91	2	21.6	0.0925	0.00000109	247

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to the LIM domain of a wide variety of LIM domain- containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. Plays a role in the development of interneurons and motor neurons in cooperation with LHX3 and ISL1. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression. Acts with LMO2 in the regulation of red blood cell development, maintaining erythroid precursors in an immature state (By similarity). {ECO:0000250|UniProtKB:P70662}.;

Recessive Scores

pRec: 0.186

Intolerance Scores

LoFtool: 0.0572
RVIS EVS: -0.43
RVIS percentile EVS: 25.15

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.943

Gene Damage Prediction

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