ELMOD1

ELMO domain containing 1, the group of ELMO domain containing

Basic information

Region (hg38): 11:107591091-107666779

Links

ENSG00000110675 ∙ NCBI:55531 ∙ OMIM:615456 ∙ HGNC:25334 ∙ Uniprot:Q8N336 ∙ 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 ELMOD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELMOD1 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in ELMOD1

This is a list of pathogenic ClinVar variants found in the ELMOD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-107630419-T-C		not specified	Uncertain significance (Sep 01, 2021)
11-107630430-G-C		not specified	Uncertain significance (Jan 26, 2022)
11-107630448-T-G		not specified	Uncertain significance (Apr 22, 2024)
11-107630453-A-G			Likely benign (Feb 01, 2023)
11-107630478-G-A		not specified	Uncertain significance (Nov 20, 2024)
11-107630501-A-T		not specified	Uncertain significance (Mar 28, 2023)
11-107630514-C-T		not specified	Uncertain significance (May 10, 2024)
11-107630714-G-A		not specified	Uncertain significance (Jun 07, 2024)
11-107631599-G-A		not specified	Uncertain significance (Apr 18, 2023)
11-107631610-G-A		not specified	Uncertain significance (Nov 21, 2022)
11-107631613-G-A		not specified	Uncertain significance (Dec 03, 2021)
11-107631667-G-A		not specified	Likely benign (Jan 20, 2023)
11-107635683-G-C		not specified	Uncertain significance (Feb 28, 2023)
11-107635694-G-A		not specified	Uncertain significance (Nov 26, 2024)
11-107650343-C-T		not specified	Uncertain significance (Oct 05, 2023)
11-107650387-C-T		not specified	Uncertain significance (Jul 20, 2021)
11-107650394-C-T		not specified	Uncertain significance (Feb 23, 2023)
11-107654186-C-T		not specified	Uncertain significance (May 31, 2023)
11-107655982-C-A		not specified	Uncertain significance (Oct 26, 2022)
11-107656019-A-G		not specified	Uncertain significance (Sep 06, 2022)
11-107665037-A-G		not specified	Uncertain significance (Nov 14, 2023)
11-107665038-T-G		not specified	Uncertain significance (Oct 12, 2022)
11-107665046-A-G		not specified	Uncertain significance (May 03, 2023)
11-107665094-G-A		not specified	Uncertain significance (Jun 18, 2021)
11-107665112-G-T		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELMOD1	protein_coding	protein_coding	ENST00000265840	11	75689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.793	0.207	124593	0	4	124597	0.0000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.984	136	172	0.789	0.00000928	2198
Missense in Polyphen		51	78.495	0.64972		957
Synonymous	1.69	44	60.7	0.725	0.00000337	577
Loss of Function	3.32	3	18.4	0.163	8.40e-7	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000182	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000183	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a GTPase-activating protein (GAP) toward guanine nucleotide exchange factors like ARL2, ARL3, ARF1 and ARF6, but not for GTPases outside the Arf family. {ECO:0000269|PubMed:17452337}.

Recessive Scores

• pRec: 0.0962

Intolerance Scores

• loftool: 0.350
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.102
• hipred: Y
• hipred_score: 0.687
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.807

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elmod1
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; immune system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: positive regulation of GTPase activity
• Cellular component: nucleoplasm;cytosol
• Molecular function: GTPase activator activity