MYCBP

MYC binding protein

Basic information

Region (hg38): 1:38862493-38873368

Links

ENSG00000214114

∙ NCBI:26292 ∙ OMIM:606535 ∙ HGNC:7554 ∙ Uniprot:Q99417 ∙ 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 MYCBP gene.

Variants pathogenicity by type

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

Variants in MYCBP

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

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

Position	Phenotype	Significance	ClinVar
1-38864696-G-A	not specified	Uncertain significance (Mar 24, 2023)	2550823
1-38866951-G-A	not specified	Uncertain significance (Apr 19, 2023)	2538909
1-38866977-G-A	not specified	Uncertain significance (Jan 14, 2025)	3876160
1-38873080-G-A	not specified	Uncertain significance (Aug 12, 2024)	3400455

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYCBP	protein_coding	protein_coding	ENST00000397572	5	18654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.845	0.153	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.930	32	50.6	0.632	0.00000254	650
Missense in Polyphen		4	8.0343	0.49786		112
Synonymous	1.33	11	18.2	0.604	8.68e-7	178
Loss of Function	2.29	0	6.12	0.00	2.55e-7	93

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Function: FUNCTION: May control the transcriptional activity of MYC. Stimulates the activation of E box-dependent transcription by MYC.;
Pathway: Glutaminolysis and Cancer;Pathways Affected in Adenoid Cystic Carcinoma;Notch signaling pathway (Consensus)

Intolerance Scores

loftool: 0.355
rvis_EVS: 0.1
rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

pHI: 0.203
hipred: Y
hipred_score: 0.645
ghis: 0.504

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mycbp
Phenotype

Zebrafish Information Network

Gene name: mycbp
Affected structure: smoothened signaling pathway
Phenotype tag: abnormal
Phenotype quality: decreased process quality

Gene ontology

Biological process: regulation of transcription, DNA-templated;spermatogenesis;positive regulation of nucleic acid-templated transcription
Cellular component: nucleus;cytoplasm;mitochondrion
Molecular function: transcription coactivator activity;protein binding