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

Summary

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

Location:: 2p11.2

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (85354769..85391748)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (85356760..85393759)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (85581892..85618871)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.

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Phenotypes

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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	not available
Hearing loss, autosomal dominant 81 MedGen: C5561972 OMIM: 619500 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

GDB:434012 (e-PCR)
- UniSTS:157204

D8S2279 (e-PCR)
- UniSTS:473907

A006X07 (e-PCR)
- UniSTS:62771

Cda02a04 (e-PCR)
- UniSTS:71263

D15S1477 (e-PCR)
- UniSTS:474482

D1S1423 (e-PCR)
- UniSTS:149619

D1S1425 (e-PCR)
- UniSTS:149621

G35510 (e-PCR)
- UniSTS:44150

G54796 (e-PCR)
- UniSTS:117879

D11S3114 (e-PCR)
- UniSTS:152207

RH41773 (e-PCR)
- UniSTS:68501

G30177 (e-PCR)
- UniSTS:62369

GDB:313783 (e-PCR)
- UniSTS:13512

D2S2699 (e-PCR)
- UniSTS:6604

A005V40 (e-PCR)
- UniSTS:55010

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

Process	Evidence Code	Pubs
involved_in auditory receptor cell development	IEA Inferred from Electronic Annotation more info
involved_in cilium assembly	IEA Inferred from Electronic Annotation more info
involved_in cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info
involved_in stereocilium maintenance	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	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

NG_051291.1 RefSeqGene

Range

5376..42355

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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

NR_138131.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC062037
NR_138132.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC062037
NR_138133.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC062037

Related

ENST00000423095.7