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

• spermatogenic failure (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYCBPAP gene.

• not_specified (128 variants)

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. These statistics are base on transcript: NM_000032133.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			114	12		126
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	114	12	0

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