ELMO3

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

Basic information

Region (hg38): 16:67199111-67204029

Links

ENSG00000102890 ∙ NCBI:79767 ∙ OMIM:606422 ∙ HGNC:17289 ∙ Uniprot:Q96BJ8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELMO3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELMO3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			62	5	1	68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			3	2		5
Total	0	0	66	8	1

Variants in ELMO3

This is a list of pathogenic ClinVar variants found in the ELMO3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-67199208-C-G		not specified	Likely benign (Aug 01, 2022)
16-67199229-G-A		not specified	Uncertain significance (Jan 07, 2025)
16-67199249-G-A		not specified	Uncertain significance (Jul 27, 2024)
16-67199250-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-67199258-G-A		not specified	Likely benign (Oct 01, 2024)
16-67199316-C-T		not specified	Uncertain significance (Nov 08, 2021)
16-67199330-G-A		not specified	Likely benign (Sep 27, 2022)
16-67199346-T-C		not specified	Uncertain significance (Dec 06, 2024)
16-67199349-T-C		not specified	Uncertain significance (Oct 10, 2023)
16-67199363-A-C			Benign (Apr 19, 2019)
16-67199369-C-T		not specified	Uncertain significance (Jun 29, 2023)
16-67199378-A-G		not specified	Uncertain significance (Apr 06, 2024)
16-67199560-C-T		not specified	Uncertain significance (Aug 17, 2022)
16-67199566-C-T		not specified	Uncertain significance (Mar 08, 2025)
16-67199587-G-A		not specified	Uncertain significance (Jun 30, 2024)
16-67199590-A-G		not specified	Uncertain significance (Jan 09, 2024)
16-67199715-C-G		not specified	Uncertain significance (Aug 28, 2024)
16-67199749-C-T		not specified	Uncertain significance (Jan 26, 2023)
16-67199755-A-G		not specified	Uncertain significance (Dec 10, 2024)
16-67199955-G-A		not specified	Uncertain significance (May 14, 2024)
16-67199999-C-G		not specified	Uncertain significance (Mar 01, 2024)
16-67199999-C-T		not specified	Uncertain significance (Mar 24, 2023)
16-67200316-G-A		not specified	Uncertain significance (Apr 04, 2024)
16-67200319-A-T		not specified	Uncertain significance (Sep 09, 2024)
16-67200350-A-T		not specified	Uncertain significance (Nov 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELMO3	protein_coding	protein_coding	ENST00000393997	20	4919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.69e-16	0.562	124264	13	1470	125747	0.00591

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.162	495	505	0.980	0.0000333	4989
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00322	0.00317
Ashkenazi Jewish	0.000413	0.000397
East Asian	0.000334	0.000272
Finnish	0.0256	0.0253
European (Non-Finnish)	0.00633	0.00614
Middle Eastern	0.000334	0.000272
South Asian	0.00368	0.00363
Other	0.00650	0.00621

dbNSFP

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}.
• Pathway: Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.893
• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.71

Haploinsufficiency Scores

• pHI: 0.181
• hipred: Y
• hipred_score: 0.544
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.385

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elmo3
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: phagocytosis;apoptotic process;cell migration
• Cellular component: cytoplasm
• Molecular function: protein binding;SH3 domain binding