ELMO1

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

Basic information

Region (hg38): 7:36852905-37449223

Links

ENSG00000155849 ∙ NCBI:9844 ∙ OMIM:606420 ∙ HGNC:16286 ∙ Uniprot:Q92556 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELMO1 gene.

• Inborn genetic diseases (21 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELMO1 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						0
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	21	0	0

Variants in ELMO1

This is a list of pathogenic ClinVar variants found in the ELMO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-36855619-T-C		not specified	Uncertain significance (Jul 06, 2021)
7-36855687-C-T		not specified	Uncertain significance (Jul 13, 2022)
7-36855738-G-A		not specified	Uncertain significance (Mar 01, 2023)
7-36861669-T-C		not specified	Uncertain significance (Dec 19, 2022)
7-36870473-G-A		not specified	Uncertain significance (Sep 27, 2022)
7-36894858-T-C		not specified	Uncertain significance (Mar 08, 2024)
7-36894876-C-T		not specified	Uncertain significance (Jun 24, 2022)
7-36895013-A-G		not specified	Uncertain significance (Feb 14, 2024)
7-37096675-C-T		not specified	Uncertain significance (Feb 14, 2023)
7-37133216-T-C		not specified	Uncertain significance (Dec 05, 2022)
7-37211429-C-T		not specified	Uncertain significance (Nov 10, 2022)
7-37211489-C-A		not specified	Uncertain significance (Sep 16, 2021)
7-37213363-A-G		not specified	Uncertain significance (May 11, 2022)
7-37216661-C-A		not specified	Uncertain significance (Jan 06, 2023)
7-37222607-C-G			Benign (Dec 11, 2017)
7-37222683-C-T		not specified	Uncertain significance (Jul 14, 2022)
7-37224993-G-A		not specified	Uncertain significance (Jul 14, 2023)
7-37233108-G-A		not specified	Uncertain significance (Nov 21, 2022)
7-37233112-C-T		not specified	Uncertain significance (Feb 23, 2023)
7-37233141-T-C		not specified	Uncertain significance (Jan 20, 2023)
7-37233165-G-A		not specified	Uncertain significance (Feb 06, 2023)
7-37259188-C-T		not specified	Uncertain significance (Jun 29, 2022)
7-37259218-T-C			Uncertain significance (Aug 24, 2023)
7-37259319-A-G		not specified	Uncertain significance (Feb 22, 2023)
7-37342626-A-G		not specified	Uncertain significance (Jan 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELMO1	protein_coding	protein_coding	ENST00000310758	21	594892

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.900	0.100	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.13	253	437	0.579	0.0000260	4875
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000537	0.0000527
Middle Eastern	0.0000546	0.0000544
South Asian	0.000105	0.0000980
Other	0.00	0.00

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. {ECO:0000269|PubMed:11595183, ECO:0000269|PubMed:12134158}.
• Pathway: Chemokine signaling pathway - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human);Chemokine signaling pathway;Signaling by PTK6;Disease;Signal Transduction;VEGFA-VEGFR2 Pathway;Host Interactions of HIV factors;HIV Infection;Fcgamma receptor (FCGR) dependent phagocytosis;TCR;Infectious disease;Innate Immune System;Immune System;Nef and signal transduction;Regulation of RAC1 activity;The role of Nef in HIV-1 replication and disease pathogenesis;Regulation of actin dynamics for phagocytic cup formation;PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases;Signaling by Non-Receptor Tyrosine Kinases;Signaling by VEGF;Signaling by Receptor Tyrosine Kinases;Neurotrophic factor-mediated Trk receptor signaling;Netrin-mediated signaling events;Signaling events mediated by focal adhesion kinase;IL8- and CXCR2-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.387
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.378
• hipred: Y
• hipred_score: 0.756
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elmo1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; reproductive system phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: elmo1
• Affected structure: thoracic duct
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: phagocytosis, engulfment;apoptotic process;cell migration;Rac protein signal transduction;actin cytoskeleton organization;Fc-gamma receptor signaling pathway involved in phagocytosis;vascular endothelial growth factor receptor signaling pathway;cell motility;regulation of defense response to virus by virus
• Cellular component: cytoplasm;cytosol;plasma membrane;membrane;guanyl-nucleotide exchange factor complex
• Molecular function: guanyl-nucleotide exchange factor activity;protein binding;SH3 domain binding