ELMOD2

ELMO domain containing 2, the group of ELMO domain containing

Basic information

Region (hg38): 4:140524167-140553770

Links

ENSG00000179387 ∙ NCBI:255520 ∙ OMIM:610196 ∙ HGNC:28111 ∙ Uniprot:Q8IZ81 ∙ 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 ELMOD2 gene.

• Inborn genetic diseases (11 variants)
• not provided (6 variants)
• not specified (4 variants)
• ELMOD2-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELMOD2 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			12	1	1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					7	7
Total	0	0	12	1	8

Variants in ELMOD2

This is a list of pathogenic ClinVar variants found in the ELMOD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-140525126-A-G			Benign (Jun 19, 2021)
4-140525508-G-A		not specified	Uncertain significance (Apr 08, 2022)
4-140525544-T-G		not specified	Likely benign (Feb 06, 2017)
4-140525563-C-G		not specified	Uncertain significance (Mar 01, 2024)
4-140525613-G-T			Benign (Nov 10, 2018)
4-140535804-G-T		not specified	Uncertain significance (Jan 22, 2024)
4-140537331-T-G			Benign (Nov 11, 2018)
4-140537486-T-A		not specified	Uncertain significance (Aug 04, 2021)
4-140537498-C-A		not specified	Uncertain significance (Dec 16, 2022)
4-140537520-G-A		ELMOD2-related disorder	Likely benign (Jun 14, 2019)
4-140537545-A-C		not specified	Benign (Feb 21, 2013)
4-140540014-A-G			Benign (Nov 10, 2018)
4-140540016-A-T			Benign (Nov 12, 2018)
4-140540196-A-C		not specified	Benign (Feb 21, 2013)
4-140540249-G-A		not specified	Uncertain significance (Oct 26, 2022)
4-140540468-T-C			Benign (Jun 18, 2021)
4-140542588-A-T		not specified	Uncertain significance (May 31, 2023)
4-140543479-A-G		not specified	Uncertain significance (May 11, 2022)
4-140543499-A-G		not specified	Uncertain significance (May 01, 2022)
4-140543512-G-A		ELMOD2-related disorder	Likely benign (May 02, 2023)
4-140543512-G-C		not specified	Uncertain significance (Dec 19, 2023)
4-140543515-A-G		not specified	Uncertain significance (Jun 03, 2022)
4-140543524-A-G		Long QT syndrome	Likely benign (-)
4-140543530-A-C		not specified	Uncertain significance (Jan 19, 2022)
4-140543551-G-A		ELMOD2-related disorder	Uncertain significance (Nov 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELMOD2	protein_coding	protein_coding	ENST00000323570	8	29613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.418	0.581	125713	0	31	125744	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.565	129	148	0.870	0.00000693	1969
Missense in Polyphen		46	60.742	0.75731		829
Synonymous	0.249	46	48.2	0.954	0.00000231	471
Loss of Function	3.10	4	18.3	0.218	0.00000102	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000212	0.000202
Middle Eastern	0.00	0.00
South Asian	0.0000762	0.0000653
Other	0.000198	0.000163

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. Regulates IFN-related antiviral responses. {ECO:0000269|PubMed:17452337, ECO:0000269|PubMed:19966137}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Lung fibrosis (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.470
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.352
• hipred: Y
• hipred_score: 0.595
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elmod2
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: positive regulation of GTPase activity;regulation of defense response to virus;defense response to virus
• Cellular component: membrane
• Molecular function: GTPase activator activity