LMBR1

protein-coding

limb development membrane protein 1

Gene summary

This gene encodes a member of the LMBR1-like membrane protein family. Another member of this protein family has been shown to be a lipocalin transmembrane receptor. A highly conserved, cis-acting regulatory module for the sonic hedgehog gene is located within an intron of this gene. Consequently, disruption of this genic region can alter sonic hedgehog expression and affect limb patterning, but it is not known if this gene functions directly in limb development. Mutations and chromosomal deletions and rearrangements in this genic region are associated with acheiropody and preaxial polydactyly, which likely result from altered sonic hedgehog expression. [provided by RefSeq, Jul 2008]

Previous symbols:
  • C7orf2

MANE transcript

NM_022458.4

Inheritance

AD, AR

ClinVar variants

P:2U:95B:33

Top phenotype

Acheiropody; Syndactyly, type IV; Laurin-Sandrow syndrome; Triphalangeal thumb, type I; Polydactyly, preaxial type II; Triphalangeal thumb with polysyndactyly; Tibia, hypoplasia or aplasia of, with polydactyly

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr7:156,668,946-156,893,216

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~224.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

triphalangeal thumb-polysyndactyly syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0017454

Submitter: PanelApp Australia

laurin-Sandrow syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007615

Submitter: PanelApp Australia

syndactyly type 4STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008515

Submitter: PanelApp Australia

laurin-Sandrow syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007615

Submitter: Orphanet

polydactyly of a triphalangeal thumbSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008270

Submitter: Orphanet

acheiropodySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008700

Submitter: Labcorp Genetics (formerly Invitae)

acheiropodySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008700

Submitter: Orphanet

syndactyly type 4SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008515

Submitter: Orphanet

acheiropodySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008700

Submitter: PanelApp Australia

polydactyly of a triphalangeal thumbSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008270

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Acheiropody; Syndactyly, type IV; Laurin-Sandrow syndrome; Triphalangeal thumb, type I; Polydactyly, preaxial type II; Triphalangeal thumb with polysyndactyly; Tibia, hypoplasia or aplasia of, with polydactylyAD/AR

Manifestation: Craniofacial; Musculoskeletal

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Comments: Some conditions may be due to variants in ZRS, a SHH-regulatory element within an LMBR1 intron

Refs: 5808544; 1132167; 1155460; 1163539; 6660253; 10937618; 10780921; 11090342; 12837695; 16059937; 17152067; 17476456; 17300748; 18463159; 18178630; 18417549; 19291772; 20068592; 20569257; 22495965; 24456159; 24965254Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LMBR1 variants in ClinVar

16 Conditions Cataloged
Holoprosencephaly 3Total: 149
not providedTotal: 139
Inborn genetic diseasesTotal: 53
Polydactyly of a triphalangeal thumbTotal: 39
SHH-related disorderTotal: 21
LMBR1-related disorderTotal: 20
not specifiedTotal: 16
AcheiropodiaTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022458.4. 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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
21
clinvar
4
clinvar
29
missense
78
clinvar
8
clinvar
86
nonsense
3
clinvar
3
start loss
0
frameshift
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
9
clinvar
10
Total1195294130

Highest pathogenic variant AF is 0.000020083158

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 90 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_022458.4RefSeqNP_071903.217MANE Select
ENST00000353442.10EnsemblENSP00000326604.717MANE Select
NM_001350953.2RefSeqNP_001337882.118Standard
NM_001350954.2RefSeqNP_001337883.113Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • embryonic digit morphogenesis

Cellular Component

  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000353442
Coding exons
17
Length
224279
Individuals with no LoFs
125641
Homozygous LoFs
0
Heterozygous LoFs
106
Defined
125747
p
0.000422
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.8492062430.8470.00001223128
Missense (PolyPhen)85108.020.78691425
Synonymous0.1978991.40.9740.00000505942
Loss of Function2.331832.30.5570.00000194382

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000130.00012rare
Latino/Admixed American0.000370.00032rare
Ashkenazi Jewish0.000600.00060rare
East Asian0.000230.00022rare
Finnish0.0000930.000092rare
European (Non-Finnish)0.000650.00063rare
South Asian0.000290.00026rare
Other0.000170.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Putative membrane receptor.;
Disease
DISEASE: Acheiropody (ACHP) [MIM:200500]: Very rare condition characterized by bilateral congenital amputations of the hands and feet. The specific malformative phenotype consists of a complete amputation of the distal epiphysis of the humerus, amputation of the tibial diaphysis and aplasia of the radius, ulna, fibula and of all the bones of the hands and feet. {ECO:0000269|PubMed:11090342}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Syndactyly 4 (SDTY4) [MIM:186200]: A form of syndactyly, a congenital anomaly of the hand or foot marked by persistence of the webbing between adjacent digits that are more or less completely attached. SDTY4 is characterized by complete bilateral syndactyly (involving all digits 1 to 5). A frequent association with polydactyly (with six metacarpals and six digits) has been reported. Feet are affected occasionally. {ECO:0000269|PubMed:18417549, ECO:0000269|PubMed:24456159}. Note=The disease is caused by mutations affecting the gene represented in this entry. Disease-causing mutations consists of duplications (89-589 kb) involving the ZPA regulatory sequence (ZRS), a SHH long-range cis-regulatory element, located in LMBR1 intron 5. The mutations do not alter normal LMBR1 expression and function, but affect SHH limb expression. {ECO:0000269|PubMed:24456159}.; DISEASE: Hypoplasia or aplasia of tibia with polydactyly (THYP) [MIM:188740]: An autosomal dominant disease characterized by hypoplastic or absent tibia, and polydactyly. {ECO:0000269|PubMed:19847792, ECO:0000269|PubMed:24777739, ECO:0000269|PubMed:24965254}. Note=The disease is caused by mutations affecting the gene represented in this entry. Disease- causing mutations are located in intron 5 of LMBR1. The mutations do not alter normal LMBR1 expression and function, but disrupt a long-range, cis-regulatory element of SHH expression contained in LMBR1 intron 5. {ECO:0000269|PubMed:19847792, ECO:0000269|PubMed:24777739, ECO:0000269|PubMed:24965254}.; DISEASE: Laurin-Sandrow syndrome (LSS) [MIM:135750]: A rare autosomal dominant disorder characterized by polysyndactyly of hands and/or feet, mirror image duplication of the feet, nasal defects, and loss of identity between fibula and tibia. Some patients do not have nasal abnormalities (segmental Laurin-Sandrow syndrome). {ECO:0000269|PubMed:24456159}. Note=The disease is caused by mutations affecting the gene represented in this entry. Disease-causing mutations consists of duplications (16-75 kb) involving the ZPA regulatory sequence (ZRS), a SHH long-range cis- regulatory element, located in LMBR1 intron 5. The mutations do not alter normal LMBR1 expression and function, but affect SHH limb expression. {ECO:0000269|PubMed:24456159}.;

Recessive Scores

pRec
0.128

Intolerance Scores

LoFtool
0.798
RVIS EVS
-0.54
RVIS percentile EVS
20.54

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.471

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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