EMC10

ER membrane protein complex subunit 10, the group of ER membrane protein complex subunits

Basic information

Region (hg38): 19:50476400-50490871

Previous symbols: [ "C19orf63" ]

Links

ENSG00000161671 ∙ NCBI:284361 ∙ OMIM:614545 ∙ HGNC:27609 ∙ Uniprot:Q5UCC4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with dysmorphic facies and variable seizures (Moderate), mode of inheritance: AR
• neurodevelopmental disorder with dysmorphic facies and variable seizures (Strong), mode of inheritance: AR
• global developmental delay with or without impaired intellectual development (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with dysmorphic facies and variable seizures	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	32869858; 33531666
Renal anomalies have been described in some individuals, but it is unclear if these are related to EMC10

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EMC10 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMC10 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				8		8
missense			18	4	1	23
nonsense		2				2
start loss						0
frameshift		1		1		2
inframe indel				1		1
splice donor/acceptor (+/-2bp)	1					1
splice region			1			1
non coding				2		2
Total	1	3	18	16	1

Highest pathogenic variant AF is 0.0000263

Variants in EMC10

This is a list of pathogenic ClinVar variants found in the EMC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50476539-G-C			Likely benign (Dec 01, 2023)
19-50476607-GC-G		Neurodevelopmental disorder with dysmorphic facies and variable seizures	Pathogenic (Sep 06, 2022)
19-50476608-C-T		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
19-50476614-C-T		Neurodevelopmental disorder with dysmorphic facies and variable seizures • EMC10-related disorder	Likely pathogenic (Oct 02, 2021)
19-50476643-G-A			Likely benign (Jul 01, 2024)
19-50476651-C-G			Likely benign (Jul 01, 2024)
19-50476658-G-A		Inborn genetic diseases	Uncertain significance (Aug 09, 2022)
19-50478955-A-C		Neurodevelopmental disorder with dysmorphic facies and variable seizures	Pathogenic (Sep 06, 2022)
19-50478957-A-G		Inborn genetic diseases	Uncertain significance (Jun 03, 2022)
19-50478980-C-T		Inborn genetic diseases	Uncertain significance (Apr 11, 2023)
19-50479028-C-T		Neurodevelopmental disorder with dysmorphic facies and variable seizures	Pathogenic (Sep 06, 2022)
19-50479032-G-A		Inborn genetic diseases	Uncertain significance (Aug 04, 2021)
19-50479052-C-T		Inborn genetic diseases	Uncertain significance (May 12, 2024)
19-50479052-CG-C		Intellectual disability • Neurodevelopmental disorder with dysmorphic facies and variable seizures	Pathogenic (Dec 17, 2022)
19-50479058-C-T		Neurodevelopmental disorder with dysmorphic facies and variable seizures	Pathogenic (Aug 22, 2023)
19-50479064-C-T		Inborn genetic diseases	Uncertain significance (Sep 06, 2022)
19-50480120-G-A		Inborn genetic diseases	Uncertain significance (Oct 05, 2021)
19-50480134-G-T			Likely benign (Mar 01, 2023)
19-50480156-C-T		Neurodevelopmental disorder with dysmorphic facies and variable seizures	Pathogenic/Likely pathogenic (Apr 27, 2022)
19-50480162-G-A			Benign (May 01, 2024)
19-50480170-G-C			Likely benign (Dec 01, 2023)
19-50480171-G-A			Likely benign (Dec 01, 2023)
19-50480180-G-A		Inborn genetic diseases	Uncertain significance (Mar 12, 2024)
19-50480193-A-G		Inborn genetic diseases	Uncertain significance (Oct 27, 2022)
19-50480214-C-T		Inborn genetic diseases	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMC10	protein_coding	protein_coding	ENST00000334976	7	6952

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.41e-11	0.0447	125660	0	68	125728	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.110	152	156	0.975	0.0000103	1581
Missense in Polyphen		59	60.117	0.98142		600
Synonymous	-0.849	81	71.8	1.13	0.00000480	570
Loss of Function	-0.178	15	14.3	1.05	9.40e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000440	0.000427
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000229	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000348	0.000334
Middle Eastern	0.000229	0.000217
South Asian	0.000481	0.000457
Other	0.000338	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes angiogenesis and tissue repair in the heart after myocardial infarction. Stimulates cardiac endothelial cell migration and outgrowth via the activation of p38 MAPK, PAK and MAPK2 signaling pathways. {ECO:0000269|PubMed:28931551}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.248
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Emc10
• Phenotype: homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; vision/eye phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: angiogenesis;positive regulation of endothelial cell proliferation;positive regulation of endothelial cell migration;positive regulation of angiogenesis;positive regulation of p38MAPK cascade
• Cellular component: extracellular region;integral component of membrane;ER membrane protein complex