ELMO1

protein-coding

engulfment and cell motility 1, the group of MicroRNA protein coding host genes|Engulfment and cell motility proteins

Gene summary

This gene encodes a member of the engulfment and cell motility protein family. These proteins interact with dedicator of cytokinesis proteins to promote phagocytosis and cell migration. Increased expression of this gene and dedicator of cytokinesis 1 may promote glioma cell invasion, and single nucleotide polymorphisms in this gene may be associated with diabetic nephropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

MANE transcript

NM_014800.11

Inheritance

ClinVar variants

U:66

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr7:36,852,906-37,449,223

External References & Databases

Ensembl (ENSG00000155849)

Transcript & Mutation Effects

hg38 • Region Span ~596.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

male infertility with azoospermia or oligozoospermia due to single gene mutationMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0018393

Submitter: King Faisal Specialist Hospital and Research Center

Alhathal et al., 2020 (PMID: 32719396) reported a missense variant in a large male infertility cohort (n=285 infertile man and case–control fertile man). Gene is scored according to ClinGen classification. Moderate with total score of 8. Single-variant analysis (3 points), experimental evidence: Animal model (4 points) (PMID: 20844538) and testicular expression (1 points) (PMID: 20958313).

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ELMO1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014800.11. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			60 clinvar			60
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	66	0	0	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 61 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014800.11	RefSeq	NP_055615.8	21	MANE Select
ENST00000310758.9	Ensembl	ENSP00000312185.4	21	MANE Select
NM_001039459.3	RefSeq	NP_001034548.1	6	Standard
NM_001206480.2	RefSeq	NP_001193409.1	21	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
elmo1	Danio rerio	Structure: thoracic duct Quality: aplastic abnormal

Gene / Model

Organism

Observed Phenotype

elmo1

Danio rerio

Structure: thoracic duct

Quality: aplastic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Chemokine signaling pathway - Homo sapiens (human)
Bacterial invasion of epithelial cells - Homo sapiens (human)
Shigellosis - Homo sapiens (human)
Chemokine signaling pathway
Signaling by PTK6

Biological Process

phagocytosis, engulfment
apoptotic process
cell migration
Rac protein signal transduction
actin cytoskeleton organization

Molecular Function

guanyl-nucleotide exchange factor activity
protein binding
SH3 domain binding

Cellular Component

cytoplasm
cytosol
plasma membrane
membrane
guanyl-nucleotide exchange factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310758
Coding exons: 21
Length: 594892
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125747
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.13	253	437	0.579	0.0000260	4875
Missense (PolyPhen)		69	172.48	0.40005		1852
Synonymous	-0.477	178	170	1.05	0.0000111	1294
Loss of Function	5.15	9	47.1	0.191	0.00000276	491

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.00011	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in cytoskeletal rearrangements required for phagocytosis of apoptotic cells and cell motility. Acts in association with DOCK1 and CRK. Was initially proposed to be required in complex with DOCK1 to activate Rac Rho small GTPases. May enhance the guanine nucleotide exchange factor (GEF) activity of DOCK1. {ECO:0000269|PubMed:11595183, ECO:0000269|PubMed:12134158}.;

Recessive Scores

pRec: 0.166

Intolerance Scores

LoFtool: 0.387
RVIS EVS: -0.53
RVIS percentile EVS: 20.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.929

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium