MEPCE

methylphosphate capping enzyme, the group of 7BS DNA/RNA methyltransferases|7SK snRNP complex

Basic information

Region (hg38): 7:100428322-100434126

Previous symbols: [ "BCDIN3" ]

Links

ENSG00000146834 ∙ NCBI:56257 ∙ OMIM:611478 ∙ HGNC:20247 ∙ Uniprot:Q7L2J0 ∙ 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 MEPCE gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEPCE 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			39	2		41
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	2	0

Variants in MEPCE

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

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

Position	Type	Phenotype	Significance	ClinVar
7-100430050-T-G		not specified	Uncertain significance (May 04, 2022)
7-100430064-C-G		not specified	Uncertain significance (Feb 10, 2022)
7-100430071-C-T		not specified	Uncertain significance (May 26, 2023)
7-100430079-A-C		not specified	Uncertain significance (Mar 06, 2023)
7-100430088-T-G		not specified	Uncertain significance (Nov 30, 2021)
7-100430100-G-A		not specified	Uncertain significance (May 23, 2024)
7-100430109-A-C		not specified	Uncertain significance (Oct 20, 2021)
7-100430127-G-A		not specified	Uncertain significance (Dec 20, 2023)
7-100430140-G-A		not specified	Uncertain significance (Sep 17, 2021)
7-100430197-C-G		not specified	Uncertain significance (Jun 12, 2023)
7-100430202-G-A		not specified	Uncertain significance (Jun 06, 2023)
7-100430287-C-A		not specified	Uncertain significance (Nov 03, 2022)
7-100430304-G-A		not specified	Uncertain significance (Apr 26, 2024)
7-100430331-G-A		not specified	Uncertain significance (Aug 10, 2021)
7-100430352-G-T		not specified	Uncertain significance (Nov 03, 2023)
7-100430404-C-T		not specified	Uncertain significance (Sep 14, 2021)
7-100430535-G-C		not specified	Uncertain significance (May 29, 2024)
7-100430578-T-G		not specified	Uncertain significance (Mar 07, 2023)
7-100430750-C-G		not specified	Uncertain significance (Apr 06, 2023)
7-100430779-C-T		not specified	Uncertain significance (May 24, 2023)
7-100430784-C-G		not specified	Uncertain significance (Nov 29, 2021)
7-100430828-C-G		not specified	Uncertain significance (Mar 01, 2023)
7-100430860-G-A		not specified	Uncertain significance (Oct 13, 2023)
7-100430865-C-T		not specified	Likely benign (Jul 28, 2021)
7-100430868-G-C		not specified	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEPCE	protein_coding	protein_coding	ENST00000310512	4	5329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00196	125615	0	3	125618	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	259	366	0.707	0.0000226	4353
Missense in Polyphen		61	140.01	0.43568		1565
Synonymous	-2.66	196	154	1.27	0.00000869	1544
Loss of Function	4.21	1	22.6	0.0442	0.00000147	239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000896	0.00000881
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that adds a methylphosphate cap at the 5'-end of 7SK snRNA, leading to stabilize it. {ECO:0000269|PubMed:17643375}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.3

Haploinsufficiency Scores

• pHI: 0.552
• hipred: Y
• hipred_score: 0.701
• ghis: 0.610

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.916

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mepce
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: mepce
• Affected structure: brain
• Phenotype tag: abnormal
• Phenotype quality: degenerate

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;RNA methylation;snRNA metabolic process;negative regulation of chromatin binding;snRNA modification;positive regulation of G1/S transition of mitotic cell cycle
• Molecular function: RNA binding;O-methyltransferase activity;RNA methyltransferase activity;S-adenosylmethionine-dependent methyltransferase activity;snRNA binding