ELMO3

protein-coding

engulfment and cell motility 3, the group of Engulfment and cell motility proteins

Gene summary

The protein encoded by this gene is similar to a C. elegans protein that functions in phagocytosis of apoptotic cells and in cell migration. Other members of this small family of engulfment and cell motility (ELMO) proteins have been shown to interact with the dedicator of cyto-kinesis 1 protein to promote phagocytosis and effect cell shape changes. [provided by RefSeq, Jul 2008]

MANE transcript

NM_024712.5

Inheritance

—

ClinVar variants

U:132B:6

Top phenotype

Ullrich congenital muscular dystrophy 1A

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr16:67,199,111-67,204,029

External References & Databases

Ensembl (ENSG00000102890)

Transcript & Mutation Effects

hg38 • Region Span ~4.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ELMO3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 128

not providedTotal: 4

Ullrich congenital muscular dystrophy 1ATotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024712.5. 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 clinvar		2
missense			127 clinvar	5 clinvar		132
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	132	6	0	138

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024712.5	RefSeq	NP_078988.3	20	MANE Select
ENST00000393997.8	Ensembl	ENSP00000377566.3	20	MANE Select
ENST00000360833.6	Ensembl	ENSP00000354077.2	19	Standard
ENST00000477898.5	Ensembl	ENSP00000458539.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Bacterial invasion of epithelial cells - Homo sapiens (human)
Shigellosis - Homo sapiens (human)

Biological Process

phagocytosis
apoptotic process
cell migration

Molecular Function

protein binding
SH3 domain binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393997
Coding exons: 20
Length: 4919
Individuals with no LoFs: 124264
Homozygous LoFs: 13
Heterozygous LoFs: 1470
Defined: 125747
p: 0.00591

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.162	495	505	0.980	0.0000333	4989
Missense (PolyPhen)		174	185.67	0.93715		1916
Synonymous	-0.834	226	211	1.07	0.0000137	1588
Loss of Function	1.71	30	41.9	0.715	0.00000214	443

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0011	notable
Latino/Admixed American	0.0021	0.0021	notable
Ashkenazi Jewish	0.00041	0.00040	rare
East Asian	0.00033	0.00027	rare
Finnish	0.026	0.025	notable
European (Non-Finnish)	0.0063	0.0061	notable
South Asian	0.0037	0.0036	notable
Other	0.0065	0.0062	notable

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 (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.893
RVIS EVS: 0.56
RVIS percentile EVS: 81.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.385

Gene Damage Prediction

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