EMID1

EMI domain containing 1, the group of EMI domain containing

Basic information

Region (hg38): 22:29205896-29259597

Links

ENSG00000186998 ∙ NCBI:129080 ∙ OMIM:608926 ∙ HGNC:18036 ∙ Uniprot:Q96A84 ∙ 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 EMID1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMID1 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			27	1		28
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	27	1	0

Variants in EMID1

This is a list of pathogenic ClinVar variants found in the EMID1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29206046-G-A		not specified	Uncertain significance (Jun 07, 2024)
22-29206048-C-T		not specified	Uncertain significance (May 09, 2022)
22-29206057-T-G		not specified	Uncertain significance (Sep 20, 2023)
22-29206114-G-A		not specified	Uncertain significance (May 31, 2023)
22-29206114-G-C		not specified	Uncertain significance (Nov 09, 2023)
22-29206120-G-A		not specified	Uncertain significance (Mar 27, 2023)
22-29214940-A-T		not specified	Uncertain significance (Apr 29, 2024)
22-29214951-C-T		not specified	Uncertain significance (Oct 05, 2023)
22-29214973-A-G		not specified	Uncertain significance (Mar 06, 2023)
22-29214982-C-A		not specified	Uncertain significance (Sep 27, 2021)
22-29214988-T-G		not specified	Uncertain significance (Dec 18, 2023)
22-29215030-C-T		not specified	Uncertain significance (Oct 12, 2021)
22-29225168-T-C		not specified	Uncertain significance (Dec 07, 2023)
22-29225169-C-T		not specified	Uncertain significance (Aug 08, 2023)
22-29225214-C-T		not specified	Uncertain significance (Nov 17, 2023)
22-29226490-G-A		not specified	Uncertain significance (Nov 18, 2023)
22-29231024-C-G		not specified	Uncertain significance (Jun 13, 2022)
22-29231050-G-A		not specified	Uncertain significance (Apr 20, 2023)
22-29231102-C-G		not specified	Uncertain significance (Oct 10, 2023)
22-29231588-C-G			Benign (Jul 13, 2018)
22-29231601-G-A		not specified	Uncertain significance (May 24, 2023)
22-29231619-G-A		not specified	Uncertain significance (Jan 09, 2024)
22-29231653-G-A		not specified	Likely benign (Sep 20, 2023)
22-29232259-C-T		not specified	Uncertain significance (Jan 26, 2023)
22-29232307-C-G		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMID1	protein_coding	protein_coding	ENST00000334018	15	53747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.06e-8	0.876	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.511	220	242	0.908	0.0000138	2753
Missense in Polyphen		71	85.933	0.82622		1056
Synonymous	-1.48	112	93.8	1.19	0.00000545	979
Loss of Function	1.64	15	23.6	0.635	0.00000108	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000171	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0781

Intolerance Scores

• loftool: 0.306
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.14

Haploinsufficiency Scores

• pHI: 0.286
• hipred: N
• hipred_score: 0.422
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0713

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emid1
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: positive regulation of cell-substrate adhesion
• Cellular component: collagen trimer;endoplasmic reticulum;Golgi apparatus;extracellular matrix