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

ENSG00000161671NCBI:284361OMIM:614545HGNC:27609Uniprot:Q5UCC4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodevelopmental disorder with dysmorphic facies and variable seizuresARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic32869858; 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
clinvar
8
missense
18
clinvar
4
clinvar
1
clinvar
23
nonsense
2
clinvar
2
start loss
0
frameshift
1
clinvar
1
clinvar
2
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
1
non coding
2
clinvar
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)2650339
19-50476607-GC-G Neurodevelopmental disorder with dysmorphic facies and variable seizures Pathogenic (Sep 06, 2022)1704220
19-50476608-C-T Inborn genetic diseases Uncertain significance (Sep 14, 2022)2311969
19-50476614-C-T Neurodevelopmental disorder with dysmorphic facies and variable seizures • EMC10-related disorder Likely pathogenic (Oct 02, 2021)1320121
19-50476643-G-A Likely benign (Jul 01, 2024)2650340
19-50476651-C-G Likely benign (Jul 01, 2024)3025286
19-50476658-G-A Inborn genetic diseases Uncertain significance (Aug 09, 2022)2383986
19-50478955-A-C Neurodevelopmental disorder with dysmorphic facies and variable seizures Pathogenic (Sep 06, 2022)1704223
19-50478957-A-G Inborn genetic diseases Uncertain significance (Jun 03, 2022)2293558
19-50478980-C-T Inborn genetic diseases Uncertain significance (Apr 11, 2023)2519955
19-50479028-C-T Neurodevelopmental disorder with dysmorphic facies and variable seizures Pathogenic (Sep 06, 2022)1704221
19-50479032-G-A Inborn genetic diseases Uncertain significance (Aug 04, 2021)2390662
19-50479052-C-T Inborn genetic diseases Uncertain significance (May 12, 2024)3275262
19-50479052-CG-C Intellectual disability • Neurodevelopmental disorder with dysmorphic facies and variable seizures Pathogenic (Dec 17, 2022)988592
19-50479058-C-T Neurodevelopmental disorder with dysmorphic facies and variable seizures Pathogenic (Aug 22, 2023)1324329
19-50479064-C-T Inborn genetic diseases Uncertain significance (Sep 06, 2022)2310535
19-50480120-G-A Inborn genetic diseases Uncertain significance (Oct 05, 2021)2209051
19-50480134-G-T Likely benign (Mar 01, 2023)2650341
19-50480156-C-T Neurodevelopmental disorder with dysmorphic facies and variable seizures Pathogenic/Likely pathogenic (Apr 27, 2022)1320119
19-50480162-G-A Benign (May 01, 2024)2650342
19-50480170-G-C Likely benign (Dec 01, 2023)2650343
19-50480171-G-A Likely benign (Dec 01, 2023)2650344
19-50480180-G-A Inborn genetic diseases Uncertain significance (Mar 12, 2024)3088546
19-50480193-A-G Inborn genetic diseases Uncertain significance (Oct 27, 2022)2353977
19-50480214-C-T Inborn genetic diseases Uncertain significance (Aug 16, 2021)2381073

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EMC10protein_codingprotein_codingENST00000334976 76952
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
9.41e-110.04471256600681257280.000270
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1101521560.9750.00001031581
Missense in Polyphen5960.1170.98142600
Synonymous-0.8498171.81.130.00000480570
Loss of Function-0.1781514.31.059.40e-7128

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004400.000427
Ashkenazi Jewish0.0001030.0000992
East Asian0.0002290.000217
Finnish0.000.00
European (Non-Finnish)0.0003480.000334
Middle Eastern0.0002290.000217
South Asian0.0004810.000457
Other0.0003380.000326

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

loftool
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_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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
Molecular function