MYCBPAP

MYCBP associated protein

Basic information

Region (hg38): 17:50508425-50531501

Links

ENSG00000136449 ∙ NCBI:84073 ∙ OMIM:609835 ∙ HGNC:19677 ∙ Uniprot:Q8TBZ2 ∙ 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 MYCBPAP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYCBPAP 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			59	7		66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	62	7	0

Variants in MYCBPAP

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

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

Position	Type	Phenotype	Significance	ClinVar
17-50508582-C-T		not specified	Uncertain significance (Jan 18, 2023)
17-50508610-C-T		not specified	Uncertain significance (Sep 23, 2023)
17-50508657-A-G		not specified	Uncertain significance (Mar 01, 2024)
17-50508682-C-T		not specified	Uncertain significance (Nov 03, 2022)
17-50516579-G-A		not specified	Uncertain significance (Jun 07, 2024)
17-50516630-C-T		not specified	Uncertain significance (Mar 21, 2023)
17-50516669-T-C		not specified	Uncertain significance (Feb 27, 2024)
17-50517318-A-G		not specified	Uncertain significance (Jan 30, 2024)
17-50517329-C-T		not specified	Uncertain significance (Sep 29, 2023)
17-50517407-C-T		not specified	Uncertain significance (Dec 18, 2023)
17-50517600-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-50517691-A-G		not specified	Uncertain significance (Mar 25, 2024)
17-50518610-A-G		not specified	Uncertain significance (Jun 16, 2023)
17-50518659-A-G		not specified	Uncertain significance (May 09, 2022)
17-50518698-G-A		not specified	Uncertain significance (Oct 18, 2021)
17-50518982-A-G		not specified	Uncertain significance (Dec 19, 2022)
17-50519015-G-A		not specified	Uncertain significance (Jun 17, 2022)
17-50519037-A-G		not specified	Uncertain significance (Mar 07, 2024)
17-50519076-G-A		not specified	Likely benign (Sep 16, 2021)
17-50519079-G-A		not specified	Likely benign (Jun 24, 2022)
17-50519691-A-G		not specified	Uncertain significance (Jul 26, 2021)
17-50519692-T-C		not specified	Uncertain significance (Jul 25, 2023)
17-50519728-G-A		not specified	Uncertain significance (May 04, 2023)
17-50519731-G-A		not specified	Uncertain significance (Jul 06, 2022)
17-50519736-A-C		not specified	Likely benign (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYCBPAP	protein_coding	protein_coding	ENST00000323776	19	23118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.49e-9	1.00	125662	0	86	125748	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.311	539	560	0.963	0.0000313	6407
Missense in Polyphen		154	177.92	0.86555		2238
Synonymous	0.697	203	216	0.940	0.0000117	1932
Loss of Function	3.59	22	49.2	0.447	0.00000263	553

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000454	0.000452
Ashkenazi Jewish	0.000115	0.0000992
East Asian	0.000878	0.000870
Finnish	0.000789	0.000786
European (Non-Finnish)	0.000259	0.000255
Middle Eastern	0.000878	0.000870
South Asian	0.000395	0.000327
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in spermatogenesis. May be involved in synaptic processes (By similarity). {ECO:0000250|UniProtKB:Q69CM7, ECO:0000269|PubMed:12151104}.

Recessive Scores

• pRec: 0.0888

Intolerance Scores

• loftool: 0.809
• rvis_EVS: 2.01
• rvis_percentile_EVS: 97.68

Haploinsufficiency Scores

• pHI: 0.0934
• hipred: N
• hipred_score: 0.271
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.176

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mycbpap

Gene ontology

• Biological process: chemical synaptic transmission;multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: cytoplasm;membrane
• Molecular function: protein binding