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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
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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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