MAGOHB

mago homolog B, exon junction complex subunit, the group of Exon junction complex

Basic information

Region (hg38): 12:10604190-10613609

Links

ENSG00000111196 ∙ NCBI:55110 ∙ OMIM:619552 ∙ HGNC:25504 ∙ Uniprot:Q96A72 ∙ 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 MAGOHB gene.

Variants pathogenicity by type

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

Variants in MAGOHB

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

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

Position	Type	Phenotype	Significance	ClinVar
12-10606295-A-C		not specified	Uncertain significance (Nov 25, 2024)
12-10606306-A-G		not specified	Uncertain significance (Mar 01, 2023)
12-10606355-C-T		not specified	Uncertain significance (Sep 11, 2024)
12-10606369-G-A		not specified	Uncertain significance (Oct 22, 2024)
12-10607844-A-T			Benign (Jul 23, 2018)
12-10607855-T-G		not specified	Uncertain significance (May 24, 2023)
12-10609881-T-C		not specified	Uncertain significance (May 25, 2022)
12-10609924-A-C		not specified	Uncertain significance (Dec 30, 2024)
12-10613507-A-T		not specified	Uncertain significance (Sep 17, 2021)
12-10613519-C-T		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGOHB	protein_coding	protein_coding	ENST00000320756	5	7611

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.327	0.659	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.778	51	69.2	0.737	0.00000308	972
Missense in Polyphen		19	23.227	0.81801		379
Synonymous	0.454	20	22.8	0.879	0.00000101	247
Loss of Function	2.07	2	8.50	0.235	4.89e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000935	0.0000924
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in mRNA splicing and in the nonsense-mediated decay (NMD) pathway. {ECO:0000250}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);Spliceosome - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Nonsense-Mediated Decay (NMD);Transport of Mature mRNA derived from an Intron-Containing Transcript;Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.595
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.197
• hipred: N
• hipred_score: 0.297
• ghis: 0.697

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.559

Mouse Genome Informatics

• Gene name: Magohb

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;mRNA splicing, via spliceosome;RNA export from nucleus;mRNA export from nucleus;RNA splicing;mRNA 3'-end processing
• Cellular component: nucleoplasm;exon-exon junction complex;neuronal cell body;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding