MAD2L1BP

MAD2L1 binding protein

Basic information

Region (hg38): 6:43629540-43640941

Links

ENSG00000124688 ∙ NCBI:9587 ∙ OMIM:618136 ∙ HGNC:21059 ∙ Uniprot:Q15013 ∙ 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 MAD2L1BP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAD2L1BP 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			18	1	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	1

Variants in MAD2L1BP

This is a list of pathogenic ClinVar variants found in the MAD2L1BP region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43636449-A-G		not specified	Likely benign (Jan 21, 2025)
6-43636458-C-A		not specified	Uncertain significance (Jan 23, 2025)
6-43636458-C-G		not specified	Uncertain significance (Dec 23, 2024)
6-43636483-G-A		not specified	Uncertain significance (Dec 05, 2024)
6-43636516-C-T		not specified	Uncertain significance (Nov 30, 2021)
6-43636524-G-A		not specified	Uncertain significance (Jan 14, 2025)
6-43636560-C-G		not specified	Uncertain significance (May 30, 2024)
6-43636569-C-T		not specified	Uncertain significance (Aug 20, 2024)
6-43636626-T-C		not specified	Uncertain significance (Feb 19, 2025)
6-43636627-A-G		not specified	Uncertain significance (Jul 20, 2021)
6-43640048-C-T		not specified	Uncertain significance (Feb 28, 2025)
6-43640049-G-A		not specified	Uncertain significance (May 14, 2024)
6-43640051-G-A		not specified	Uncertain significance (Mar 16, 2024)
6-43640151-C-T		not specified	Uncertain significance (Dec 07, 2021)
6-43640253-G-A		not specified	Uncertain significance (Oct 12, 2021)
6-43640273-C-T		not specified	Uncertain significance (Oct 29, 2024)
6-43640274-G-A		not specified	Uncertain significance (Mar 15, 2024)
6-43640298-C-T			Benign (Dec 31, 2019)
6-43640319-A-C		not specified	Uncertain significance (Dec 21, 2024)
6-43640321-G-T		not specified	Uncertain significance (Nov 01, 2022)
6-43640406-G-A		not specified	Uncertain significance (Dec 22, 2024)
6-43640417-C-T		not specified	Uncertain significance (Oct 30, 2023)
6-43640439-C-T		not specified	Uncertain significance (May 24, 2023)
6-43640508-T-C		not specified	Uncertain significance (Jan 29, 2024)
6-43640525-C-T		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAD2L1BP	protein_coding	protein_coding	ENST00000451025	4	11413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-8	0.216	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.539	150	170	0.884	0.00000980	1958
Missense in Polyphen		50	67.408	0.74175		790
Synonymous	0.505	60	65.2	0.920	0.00000361	629
Loss of Function	0.412	13	14.7	0.884	0.00000110	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000130	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function to silence the spindle checkpoint and allow mitosis to proceed through anaphase by binding MAD2L1 after it has become dissociated from the MAD2L1-CDC20 complex. {ECO:0000269|PubMed:18022368}.

Recessive Scores

• pRec: 0.0775

Intolerance Scores

• loftool: 0.313
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.127
• hipred: Y
• hipred_score: 0.549
• ghis: 0.574

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.979

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mad2l1bp

Gene ontology

• Biological process: mitotic cell cycle checkpoint;regulation of exit from mitosis
• Cellular component: nucleus;nucleolus;cytoplasm;spindle;nuclear membrane
• Molecular function: protein binding