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    ELMOD3 ELMO domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 84173, updated on 3-Apr-2024

    Summary

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    Official Symbol
    ELMOD3provided by HGNC
    Official Full Name
    ELMO domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:26158
    See related
    Ensembl:ENSG00000115459 MIM:615427; AllianceGenome:HGNC:26158
    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
    LST3; RBED1; RBM29; DFNA81; DFNB88
    Summary
    This gene encodes a member of the engulfment and cell motility family of GTPase-activating proteins that regulate Arf GTPase proteins. Members of this family are defined by a conserved engulfment and cell motility domain. In rat cochlea, the encoded protein is found in stereocilia, kinocilia and cuticular plate of developing hair cells suggesting a function for this protein in cochlear sensory cells. An allelic variant of this family has been associated with autosomal recessive nonsyndromic deafness-88 in humans. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
    Expression
    Ubiquitous expression in fat (RPKM 29.3), skin (RPKM 5.6) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2p11.2
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (85354769..85391748)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (85356760..85393759)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (85581892..85618871)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene phosphatidylethanolamine binding protein 1 pseudogene 2 Neighboring gene retinol saturase Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:85581653-85582154 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:85582155-85582654 Neighboring gene RNA, 7SL, cytoplasmic 113, pseudogene Neighboring gene U7 small nuclear RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85628953-85629452 Neighboring gene capping actin protein, gelsolin like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11697 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:85640593-85641094 Neighboring gene uncharacterized LOC105374841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16124 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85645284-85645819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16126 Neighboring gene SH2 domain containing 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85658733-85659404 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85659405-85660075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85660076-85660746

    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. ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing loss. Li W, et al. Hum Genet, 2018 Apr. PMID 29713870
    2. An alteration in ELMOD3, an Arl2 GTPase-activating protein, is associated with hearing impairment in humans. Jaworek TJ, et al. PLoS Genet, 2013. PMID 24039609, Free PMC Article
    3. ELMO domains, evolutionary and functional characterization of a novel GTPase-activating protein (GAP) domain for Arf protein family GTPases. East MP, et al. J Biol Chem, 2012 Nov 16. PMID 23014990, Free PMC Article
    4. ELMOD3-SH2D6 gene fusion as a possible co-star actor in autism spectrum disorder scenario. Loi E, et al. J Cell Mol Med, 2020 Jan. PMID 31800155, Free PMC Article
    5. Characterization of recombinant ELMOD (cell engulfment and motility domain) proteins as GTPase-activating proteins (GAPs) for ARF family GTPases. Ivanova AA, et al. J Biol Chem, 2014 Apr 18. PMID 24616099, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Gene regulation analysis of patient-derived iPSCs and its CRISPR-corrected control provides a new tool for studying perturbations of ELMOD3 c.512A>G mutation during the development of inherited hearing loss.
      Title: Gene regulation analysis of patient-derived iPSCs and its CRISPR-corrected control provides a new tool for studying perturbations of ELMOD3 c.512A>G mutation during the development of inherited hearing loss.
    2. ELMOD3-SH2D6 gene fusion as a possible co-star actor in autism spectrum disorder scenario.
      Title: ELMOD3-SH2D6 gene fusion as a possible co-star actor in autism spectrum disorder scenario.
    3. the analysis of the stability of the wild-type (WT) and mutant ELMOD3 protein shows that the decay of p.His171Arg is faster than that of the WT, suggesting a shorter halflife of the c.512A > G variant. A novel variant in the ELMOD3 gene, encoding a member of the engulfment and cell motility (ELMO) family
      Title: ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing loss.
    4. The non-opioid sigma-1 receptor (S1R) was identified as a novel effector of GAP activity of ELMOD1-3 proteins as its direct binding to either ELMOD1 or ELMOD2 resulted in loss of GAP activity.
      Title: Characterization of recombinant ELMOD (cell engulfment and motility domain) proteins as GTPase-activating proteins (GAPs) for ARF family GTPases.
    5. Collectively, our data provide the first insights into the expression and biochemical properties of ELMOD3 and highlight its functional links to sound perception and actin cytoskeleton.
      Title: An alteration in ELMOD3, an Arl2 GTPase-activating protein, is associated with hearing impairment in humans.
    Submit: New GeneRIF Correction

    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
    Autosomal recessive nonsyndromic hearing loss 88
    MedGen: C2829267 OMIM: 615429 GeneReviews: Not available
    		Compare labs
    Hearing loss, autosomal dominant 81
    MedGen: C5561972 OMIM: 619500 GeneReviews: Not available
    		Compare labs

    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

    • FLJ21977, FLJ35601, MGC111036

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in kinocilium IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in stereocilium IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ELMO domain-containing protein 3
    Names
    ELMO/CED-12 domain containing 3
    RNA binding motif and ELMO/CED-12 domain 1
    RNA-binding motif and ELMO domain-containing protein 1
    RNA-binding motif protein 29
    deafness, autosomal recessive 88
    liver-specific organic anion transporter 3TM12
    organic anion transporter LST-3b

    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_051291.1 RefSeqGene

      Range
      5376..42355
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001135021.2 → NP_001128493.1  ELMO domain-containing protein 3 isoform b

      See identical proteins and their annotated locations for NP_001128493.1

      Status: REVIEWED

      Source sequence(s)
      AF258573, AK025630, BC112324
      Consensus CDS
      CCDS46352.1
      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8
      Related
      ENSP00000386248.3, ENST00000409344.7
      Conserved Domains (1) summary
      pfam04727
      Location:159 → 308
      ELMO_CED12; ELMO/CED-12 family

    2. NM_001135022.2 → NP_001128494.1  ELMO domain-containing protein 3 isoform b

      See identical proteins and their annotated locations for NP_001128494.1

      Status: REVIEWED

      Source sequence(s)
      AF258573, AK025630, BC010991, DA294897
      Consensus CDS
      CCDS46352.1
      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8
      Related
      ENSP00000387139.3, ENST00000409013.8
      Conserved Domains (1) summary
      pfam04727
      Location:159 → 308
      ELMO_CED12; ELMO/CED-12 family

    3. NM_001135023.2 → NP_001128495.1  ELMO domain-containing protein 3 isoform b

      See identical proteins and their annotated locations for NP_001128495.1

      Status: REVIEWED

      Source sequence(s)
      AF258573, AK025630, BC112324
      Consensus CDS
      CCDS46352.1
      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8
      Related
      ENSP00000377434.4, ENST00000393852.8
      Conserved Domains (1) summary
      pfam04727
      Location:159 → 308
      ELMO_CED12; ELMO/CED-12 family

    4. NM_001329791.2 → NP_001316720.1  ELMO domain-containing protein 3 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC062037
      Consensus CDS
      CCDS46352.1
      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8
      Conserved Domains (1) summary
      pfam04727
      Location:159 → 308
      ELMO_CED12; ELMO/CED-12 family

    5. NM_001329792.2 → NP_001316721.1  ELMO domain-containing protein 3 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC062037
      Consensus CDS
      CCDS46352.1
      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8
      Conserved Domains (1) summary
      pfam04727
      Location:159 → 308
      ELMO_CED12; ELMO/CED-12 family

    6. NM_001329793.2 → NP_001316722.1  ELMO domain-containing protein 3 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC062037
      Consensus CDS
      CCDS46352.1
      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8
      Conserved Domains (1) summary
      pfam04727
      Location:159 → 308
      ELMO_CED12; ELMO/CED-12 family

    7. NM_032213.5 → NP_115589.2  ELMO domain-containing protein 3 isoform a

      See identical proteins and their annotated locations for NP_115589.2

      Status: REVIEWED

      Source sequence(s)
      AC062037
      Consensus CDS
      CCDS1973.1
      Related
      ENSP00000318264.7, ENST00000315658.11

    RNA

    1. NR_138131.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC062037

    2. NR_138132.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC062037

    3. NR_138133.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC062037
      Related
      ENST00000423095.7

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      85354769..85391748
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445971.1 → XP_047301927.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    2. XM_047445972.1 → XP_047301928.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    3. XM_047445973.1 → XP_047301929.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8
      Related
      ENSP00000386304.2, ENST00000409890.6

    4. XM_047445975.1 → XP_047301931.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    5. XM_047445974.1 → XP_047301930.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    6. XM_047445976.1 → XP_047301932.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8
      Related
      ENST00000490508.5

    7. XM_047445966.1 → XP_047301922.1  ELMO domain-containing protein 3 isoform X1

    8. XM_047445967.1 → XP_047301923.1  ELMO domain-containing protein 3 isoform X1

    9. XM_047445965.1 → XP_047301921.1  ELMO domain-containing protein 3 isoform X1

    10. XM_047445968.1 → XP_047301924.1  ELMO domain-containing protein 3 isoform X1

    11. XM_024453169.2 → XP_024308937.1  ELMO domain-containing protein 3 isoform X1

      Conserved Domains (1) summary
      pfam04727
      Location:155 → 308
      ELMO_CED12; ELMO/CED-12 family

    12. XM_024453170.2 → XP_024308938.1  ELMO domain-containing protein 3 isoform X1

      Conserved Domains (1) summary
      pfam04727
      Location:155 → 308
      ELMO_CED12; ELMO/CED-12 family

    13. XM_047445963.1 → XP_047301919.1  ELMO domain-containing protein 3 isoform X1

    14. XM_047445964.1 → XP_047301920.1  ELMO domain-containing protein 3 isoform X1

    15. XM_047445969.1 → XP_047301925.1  ELMO domain-containing protein 3 isoform X1

    16. XM_024453171.2 → XP_024308939.1  ELMO domain-containing protein 3 isoform X1

      Conserved Domains (1) summary
      pfam04727
      Location:155 → 308
      ELMO_CED12; ELMO/CED-12 family

    17. XM_047445977.1 → XP_047301933.1  ELMO domain-containing protein 3 isoform X2

      Related
      ENSP00000407599.3, ENST00000446464.7

    18. XM_047445978.1 → XP_047301934.1  ELMO domain-containing protein 3 isoform X2

      Related
      ENSP00000401984.2, ENST00000444108.7

    19. XM_047445979.1 → XP_047301935.1  ELMO domain-containing protein 3 isoform X3

      Related
      ENSP00000386257.2, ENST00000409331.6

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791763.1 Reference GRCh38.p14 PATCHES

      Range
      281007..283491
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      85356760..85393759
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054344134.1 → XP_054200109.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    2. XM_054344135.1 → XP_054200110.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    3. XM_054344136.1 → XP_054200111.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    4. XM_054344138.1 → XP_054200113.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    5. XM_054344137.1 → XP_054200112.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    6. XM_054344139.1 → XP_054200114.1  ELMO domain-containing protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B8ZZD6, D6W5K4, Q2M1K3, Q2XSU3, Q2XSU4, Q8NAC1, Q8TCK4, Q8WV70, Q8WY75, Q96FG2, Q9H6Q8

    7. XM_054344129.1 → XP_054200104.1  ELMO domain-containing protein 3 isoform X1

    8. XM_054344131.1 → XP_054200106.1  ELMO domain-containing protein 3 isoform X1

    9. XM_054344128.1 → XP_054200103.1  ELMO domain-containing protein 3 isoform X1

    10. XM_054344132.1 → XP_054200107.1  ELMO domain-containing protein 3 isoform X1

    11. XM_054344127.1 → XP_054200102.1  ELMO domain-containing protein 3 isoform X1

    12. XM_054344125.1 → XP_054200100.1  ELMO domain-containing protein 3 isoform X1

    13. XM_054344130.1 → XP_054200105.1  ELMO domain-containing protein 3 isoform X1

    14. XM_054344123.1 → XP_054200098.1  ELMO domain-containing protein 3 isoform X1

    15. XM_054344124.1 → XP_054200099.1  ELMO domain-containing protein 3 isoform X1

    16. XM_054344133.1 → XP_054200108.1  ELMO domain-containing protein 3 isoform X1

    17. XM_054344126.1 → XP_054200101.1  ELMO domain-containing protein 3 isoform X1

    18. XM_054344140.1 → XP_054200115.1  ELMO domain-containing protein 3 isoform X2

    19. XM_054344141.1 → XP_054200116.1  ELMO domain-containing protein 3 isoform X2

    20. XM_054344142.1 → XP_054200117.1  ELMO domain-containing protein 3 isoform X3

    21. XM_054344143.1 → XP_054200118.1  ELMO domain-containing protein 3 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96FG2.2 GenPept UniProtKB/Swiss-Prot:Q96FG2

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