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    LMBR1 limb development membrane protein 1 [ Homo sapiens (human) ]

    Gene ID: 64327, updated on 11-Apr-2024

    Summary

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    Official Symbol
    LMBR1provided by HGNC
    Official Full Name
    limb development membrane protein 1provided by HGNC
    Primary source
    HGNC:HGNC:13243
    See related
    Ensembl:ENSG00000105983 MIM:605522; AllianceGenome:HGNC:13243
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LSS; TPT; ZRS; ACHP; PPD2; THYP; DIF14; TPTPS; C7orf2
    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]
    Expression
    Ubiquitous expression in testis (RPKM 9.4), adrenal (RPKM 8.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LMBR1 in Genome Data Viewer
    Location:
    7q36.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (156669012..156893183, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (157856727..158080951, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (156461706..156685877, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RNF32 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:156332839-156333338 Neighboring gene long intergenic non-protein coding RNA 244 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:156377606-156378120 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:156378121-156378635 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:156400279-156400790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26908 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:156412155-156412844 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:156412845-156413534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:156432899-156433490 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:156443773-156443992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26910 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:156449836-156451035 Neighboring gene ribosomal protein L26 pseudogene 23 Neighboring gene ring finger protein 32 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26911 Neighboring gene Sharpr-MPRA regulatory region 13578 Neighboring gene ZRS shadow enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26913 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:156613382-156613882 Neighboring gene ZPA regulatory sequence Neighboring gene ReSE screen-validated silencer GRCh37_chr7:156647348-156647581 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:156657413-156657607 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:156665750-156665992 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:156670519-156670739 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18853 Neighboring gene uncharacterized LOC102723795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26914 Neighboring gene RNA, U4 small nuclear 31, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:156707384-156708583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26917 Neighboring gene uncharacterized threonine-rich GPI-anchored glycoprotein PJ4664.02-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Large duplication in LMBR1 gene in a large Chinese pedigree with triphalangeal thumb polysyndactyly syndrome. Xu J, et al. Am J Med Genet A, 2020 Sep. PMID 32662247
    2. Variable expression of subclinical phenotypes instead of reduced penetrance in families with mild triphalangeal thumb phenotypes. Potuijt JWP, et al. J Med Genet, 2020 Oct. PMID 32179704, Free PMC Article
    3. Intriguing balancing selection on the intron 5 region of LMBR1 in human population. He F, et al. PLoS One, 2008 Aug 13. PMID 18698406, Free PMC Article
    4. Linkage of preaxial polydactyly type 2 to 7q36. Hing AV, et al. Am J Med Genet, 1995 Aug 28. PMID 8533803
    5. A novel mutation (g.106737G>T) in zone of polarizing activity regulatory sequence (ZRS) causes variable limb phenotypes in Werner mesomelia. Girisha KM, et al. Am J Med Genet A, 2014 Apr. PMID 24478176

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Variable expression of subclinical phenotypes instead of reduced penetrance in families with mild triphalangeal thumb phenotypes.
      Title: Variable expression of subclinical phenotypes instead of reduced penetrance in families with mild triphalangeal thumb phenotypes.
    2. Large duplication in LMBR1 gene in a large Chinese pedigree with triphalangeal thumb polysyndactyly syndrome.
      Title: Large duplication in LMBR1 gene in a large Chinese pedigree with triphalangeal thumb polysyndactyly syndrome.
    3. Results identify a novel g.101779T>A variant segregating with all individuals affected with preaxial polydactyly type 1(PPDI).
      Title: A novel ZRS variant causes preaxial polydactyly type I by increased sonic hedgehog expression in the developing limb bud.
    4. These include a patient with hypoplastic phalanges and absent hallux bilaterally with de novo deletion of 11.9 Mb on 7p21.1-22.1 spanning 63 genes including RAC1, another patient with severe Holt-Oram syndrome and a large de novo deletion 2.2 Mb on 12q24.13-24.21 spanning 20 genes including TBX3 and TBX5, and a third patient with acheiropodia who had a nullizygous deletion of 102 kb on 7q36.3 spanning LMBR1
      Title: Novel copy number variants and major limb reduction malformation: Report of three cases.
    5. A novel ZRS mutation found in the Mexican population, 402C>T, suggests that a dosage effect exists for this mutation.
      Title: A novel ZRS mutation leads to preaxial polydactyly type 2 in a heterozygous form and Werner mesomelic syndrome in a homozygous form.
    6. Data describe extensive variation in limb phenotype in a large family and report on a novel sequence variation NG_009240.1: g.106737G>T (traditional nomenclature: ZRS404G>T) in the ZRS within the LMBR1 gene.
      Title: A novel mutation (g.106737G>T) in zone of polarizing activity regulatory sequence (ZRS) causes variable limb phenotypes in Werner mesomelia.
    7. Review of the literature and cases in a Chinese family confirm genetic homogeneity (duplication of ZRS wintin intron 5 of LMBR1) of syndactyly type IV and triphalangeal thumb-polysyndactyly syndrome.
      Title: Confirmation of genetic homogeneity of syndactyly type IV and triphalangeal thumb-polysyndactyly syndrome in a Chinese family and review of the literature.
    8. report of a new point mutation within the ZRS in a family with digit malformations including triphalangeal thumb, pre-axial polydactyly and post-axial polydactyly; heterozygous C>A mutation at position 287 of the ZRS enhancer was detected in all affected subjects and is absent from four unaffected family members
      Title: A novel ZRS mutation in a Balochi tribal family with triphalangeal thumb, pre-axial polydactyly, post-axial polydactyly, and syndactyly.
    9. A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb.
      Title: A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb.
    10. Effect on transcription factor binding of a novel ZRS point mutation (463T>G) in a Pakistani family with preaxial polydactyly and triphalangeal thumb.
      Title: Preaxial polydactyly/triphalangeal thumb is associated with changed transcription factor-binding affinity in a family with a novel point mutation in the long-range cis-regulatory element ZRS.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Acheiropodia
    MedGen: C0265559 OMIM: 200500 GeneReviews: Not available
    		Compare labs
    Laurin-Sandrow syndrome
    MedGen: C1851100 OMIM: 135750 GeneReviews: Not available
    		Compare labs
    Syndactyly type 4
    MedGen: C1861355 OMIM: 186200 GeneReviews: Not available
    		Compare labs
    Triphalangeal thumb with polysyndactyly syndrome
    MedGen: C5779878 OMIM: 190605 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11665

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transmembrane signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in embryonic digit morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    limb region 1 protein homolog
    Names
    differentiation-related gene 14 protein
    limb region 1 homolog

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009240.2 RefSeqGene

      Range
      5026..220418
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001350953.2 → NP_001337882.1  limb region 1 protein homolog isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC005534, AC007075, AC007097
      UniProtKB/TrEMBL
      H0Y6V6
      Related
      ENSP00000408256.1, ENST00000415428.5
      Conserved Domains (1) summary
      pfam04791
      Location:19 → 491
      LMBR1; LMBR1-like membrane protein

    2. NM_001350954.2 → NP_001337883.1  limb region 1 protein homolog isoform c

      Status: REVIEWED

      Source sequence(s)
      AC005534, AC007075, AC007097
      Conserved Domains (1) summary
      pfam04791
      Location:8 → 317
      LMBR1; LMBR1-like membrane protein

    3. NM_001350955.2 → NP_001337884.1  limb region 1 protein homolog isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4), as well as variant 5, encodes isoform d.
      Source sequence(s)
      AC005534, AC007075, AC007097
      Conserved Domains (1) summary
      pfam04791
      Location:33 → 298
      LMBR1; LMBR1-like membrane protein

    4. NM_001350956.2 → NP_001337885.1  limb region 1 protein homolog isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5), as well as variant 4, encodes isoform d.
      Source sequence(s)
      AC005534, AC007075, AC007097
      Conserved Domains (1) summary
      pfam04791
      Location:33 → 298
      LMBR1; LMBR1-like membrane protein

    5. NM_001350957.2 → NP_001337886.1  limb region 1 protein homolog isoform e

      Status: REVIEWED

      Source sequence(s)
      AC005534, AC007075, AC007097
      Conserved Domains (1) summary
      pfam04791
      Location:1 → 287
      LMBR1; LMBR1-like membrane protein

    6. NM_001350958.2 → NP_001337887.1  limb region 1 protein homolog isoform f

      Status: REVIEWED

      Source sequence(s)
      AC005534, AC007075, AC007097
      UniProtKB/TrEMBL
      Q8NDP7
      Conserved Domains (1) summary
      pfam04791
      Location:33 → 258
      LMBR1; LMBR1-like membrane protein

    7. NM_001363409.2 → NP_001350338.1  limb region 1 protein homolog isoform g

      Status: REVIEWED

      Source sequence(s)
      AC005534, AC007075, BC017663, DA238712, EB388873, H18430
      UniProtKB/TrEMBL
      H0Y6V6
      Conserved Domains (1) summary
      pfam04791
      Location:19 → 451
      LMBR1; LMBR1-like membrane protein

    8. NM_001363410.2 → NP_001350339.1  limb region 1 protein homolog isoform h

      Status: REVIEWED

      Source sequence(s)
      AC005534, AC007075, AC007097
      UniProtKB/TrEMBL
      A8K4S2
      Conserved Domains (1) summary
      pfam04791
      Location:19 → 410
      LMBR1; LMBR1-like membrane protein

    9. NM_001363411.2 → NP_001350340.1  limb region 1 protein homolog isoform i

      Status: REVIEWED

      Source sequence(s)
      AC005534, AC007075, AC007097
      Conserved Domains (1) summary
      pfam04791
      Location:1 → 327
      LMBR1; LMBR1-like membrane protein

    10. NM_001363412.2 → NP_001350341.1  limb region 1 protein homolog isoform j

      Status: REVIEWED

      Source sequence(s)
      AC005534, AK299753, BC017663, DA238712, H18430
      UniProtKB/TrEMBL
      B7Z633
      Conserved Domains (1) summary
      pfam04791
      Location:35 → 389
      LMBR1; LMBR1-like membrane protein

    11. NM_001363413.2 → NP_001350342.1  limb region 1 protein homolog isoform d

      Status: REVIEWED

      Source sequence(s)
      AC005534, BC017663, BC063649, DA238712, H18430
      Conserved Domains (1) summary
      pfam04791
      Location:33 → 298
      LMBR1; LMBR1-like membrane protein

    12. NM_022458.4 → NP_071903.2  limb region 1 protein homolog isoform b

      See identical proteins and their annotated locations for NP_071903.2

      Status: REVIEWED

      Source sequence(s)
      AC005534, BC017663, DA238712, H18430
      Consensus CDS
      CCDS5945.1
      UniProtKB/Swiss-Prot
      A4D242, Q8N3E3, Q8WVP7, Q96QZ5, Q9H5N0, Q9HAG9, Q9UDN5, Q9Y6U2
      UniProtKB/TrEMBL
      A8K4S2
      Related
      ENSP00000326604.7, ENST00000353442.10
      Conserved Domains (1) summary
      pfam04791
      Location:19 → 450
      LMBR1; LMBR1-like membrane protein

    RNA

    1. NR_146958.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC005534, AC007075, AC007097

    2. NR_146959.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC005534, AC007075, AC007097

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      156669012..156893183 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005249558.3 → XP_005249615.1  limb region 1 protein homolog isoform X6

      Conserved Domains (1) summary
      pfam04791
      Location:26 → 262
      LMBR1; LMBR1-like membrane protein

    2. XM_017012515.3 → XP_016868004.1  limb region 1 protein homolog isoform X5

    3. XM_047420703.1 → XP_047276659.1  limb region 1 protein homolog isoform X1

    4. XM_047420705.1 → XP_047276661.1  limb region 1 protein homolog isoform X3

    5. XM_047420704.1 → XP_047276660.1  limb region 1 protein homolog isoform X2

    6. XM_047420706.1 → XP_047276662.1  limb region 1 protein homolog isoform X4

    RNA

    1. XR_007060137.1 RNA Sequence

    2. XR_007060136.1 RNA Sequence

    3. XR_007060135.1 RNA Sequence

    4. XR_007060134.1 RNA Sequence

    5. XR_007060133.1 RNA Sequence

    6. XR_007060131.1 RNA Sequence

    7. XR_007060130.1 RNA Sequence

    8. XR_007060132.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      157856727..158080951 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358789.1 → XP_054214764.1  limb region 1 protein homolog isoform X1

    2. XM_054358791.1 → XP_054214766.1  limb region 1 protein homolog isoform X3

    3. XM_054358790.1 → XP_054214765.1  limb region 1 protein homolog isoform X2

    4. XM_054358792.1 → XP_054214767.1  limb region 1 protein homolog isoform X4

    RNA

    1. XR_008487732.1 RNA Sequence

    2. XR_008487731.1 RNA Sequence

    3. XR_008487730.1 RNA Sequence

    4. XR_008487728.1 RNA Sequence

    5. XR_008487729.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WVP7.1 GenPept UniProtKB/Swiss-Prot:Q8WVP7

    Gene LinkOut

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