ELMOD3

ELMO domain containing 3, the group of RNA binding motif containing|ELMO domain containing

Basic information

Region (hg38): 2:85354394-85391752

Previous symbols: [ "RBM29", "RBED1", "DFNB88" ]

Links

ENSG00000115459 ∙ NCBI:84173 ∙ OMIM:615427 ∙ HGNC:26158 ∙ Uniprot:Q96FG2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 88 (Moderate), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 88 (Limited), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Limited), mode of inheritance: AD
• nonsyndromic genetic hearing loss (Limited), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 88 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 88	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	24039609; 29713870

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELMOD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELMOD3 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				26	6	32
missense			42	8	5	55
nonsense			6			6
start loss						0
frameshift			3			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	2		4
non coding			2	25	20	47
Total	0	0	53	59	31

Variants in ELMOD3

This is a list of pathogenic ClinVar variants found in the ELMOD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-85354426-T-C		not specified	Uncertain significance (Mar 12, 2024)
2-85354463-G-A			Benign (Jul 12, 2018)
2-85356750-G-A			Likely benign (Aug 18, 2019)
2-85356880-CA-C			Likely benign (Oct 02, 2019)
2-85356880-C-CA			Likely benign (Oct 09, 2019)
2-85356880-C-CAA			Benign (Oct 22, 2019)
2-85357204-T-C			Likely benign (Jul 07, 2023)
2-85357213-T-C			Likely benign (Jul 08, 2022)
2-85357244-G-A		not specified	Uncertain significance (Apr 05, 2023)
2-85357256-A-C			Uncertain significance (Nov 22, 2022)
2-85357266-C-T			Likely benign (Dec 01, 2023)
2-85362171-T-C			Likely benign (Jan 04, 2024)
2-85362187-G-A			Uncertain significance (Jul 08, 2023)
2-85362189-G-A			Uncertain significance (Aug 10, 2023)
2-85362209-T-G			Uncertain significance (Sep 19, 2022)
2-85362243-G-A		ELMOD3-related disorder • not specified	Uncertain significance (May 16, 2023)
2-85362254-A-G			Likely benign (Aug 23, 2022)
2-85362265-G-A			Uncertain significance (Jun 03, 2023)
2-85362273-C-G			Likely benign (Dec 06, 2023)
2-85362389-T-C			Likely benign (Jan 25, 2019)
2-85362912-C-T			Benign (Dec 17, 2018)
2-85363076-A-G			Likely benign (Jul 29, 2020)
2-85363084-G-A			Benign (Oct 05, 2023)
2-85363099-C-T			Likely benign (Jul 18, 2018)
2-85363115-C-T			Uncertain significance (Feb 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELMOD3	protein_coding	protein_coding	ENST00000315658	10	37359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.04e-16	0.00350	125643	0	105	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.397	200	216	0.924	0.0000117	2539
Missense in Polyphen		63	75.951	0.82948		904
Synonymous	1.00	73	84.7	0.862	0.00000461	777
Loss of Function	-0.527	22	19.5	1.13	0.00000107	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00137	0.00137
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000309	0.000308
Middle Eastern	0.000544	0.000544
South Asian	0.000949	0.000948
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a GTPase-activating protein (GAP) for ARL2 with low specific activity. {ECO:0000269|PubMed:24039609}.

Intolerance Scores

• loftool: 0.999
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.61

Haploinsufficiency Scores

• pHI: 0.167
• hipred: N
• hipred_score: 0.144
• ghis: 0.385

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.300

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Elmod3

Gene ontology

• Biological process: positive regulation of GTPase activity
• Cellular component: cytoplasm;cytoskeleton;stereocilium;kinocilium
• Molecular function: GTPase activator activity;protein binding