MYCT1

MYC target 1

Basic information

Region (hg38): 6:152697897-152724569

Links

ENSG00000120279 ∙ NCBI:80177 ∙ OMIM:616805 ∙ HGNC:23172 ∙ Uniprot:Q8N699 ∙ 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 MYCT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYCT1 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				1		1
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in MYCT1

This is a list of pathogenic ClinVar variants found in the MYCT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-152697907-G-A		not specified	Likely benign (Aug 10, 2021)
6-152697916-T-G		not specified	Uncertain significance (Oct 11, 2024)
6-152697919-A-T		not specified	Uncertain significance (Feb 06, 2024)
6-152697990-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-152698054-A-G		not specified	Uncertain significance (Jun 22, 2023)
6-152721788-A-T			Likely benign (Dec 01, 2023)
6-152721813-T-C		not specified	Uncertain significance (Mar 01, 2024)
6-152721838-G-C		not specified	Uncertain significance (Oct 21, 2021)
6-152721844-G-C		not specified	Uncertain significance (Oct 26, 2021)
6-152721849-C-G		not specified	Uncertain significance (Nov 03, 2023)
6-152721882-A-G		not specified	Uncertain significance (May 05, 2022)
6-152721898-A-G		not specified	Uncertain significance (Oct 11, 2024)
6-152721970-T-G		not specified	Uncertain significance (Mar 18, 2024)
6-152722065-C-T		not specified	Uncertain significance (Apr 04, 2023)
6-152722068-C-T		not specified	Uncertain significance (Jun 24, 2022)
6-152722075-C-T		not specified	Uncertain significance (Jun 07, 2024)
6-152722134-A-T		not specified	Uncertain significance (Jan 23, 2024)
6-152722204-C-T		not specified	Uncertain significance (Aug 16, 2022)
6-152722222-A-T		not specified	Uncertain significance (Jan 16, 2024)
6-152722224-T-G		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYCT1	protein_coding	protein_coding	ENST00000367245	2	26673

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000366	0.632	125661	0	64	125725	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.131	127	123	1.03	0.00000631	1518
Missense in Polyphen		51	53	0.96227		616
Synonymous	-0.141	47	45.8	1.03	0.00000230	497
Loss of Function	0.677	6	8.08	0.743	5.62e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000493	0.000493
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate certain MYC target genes, MYC seems to be a direct upstream transcriptional activator. Does not seem to significantly affect growth cell capacity. Overexpression seems to mediate many of the known phenotypic features associated with MYC, including promotion of apoptosis, alteration of morphology, enhancement of anchorage-independent growth, tumorigenic conversion, promotion of genomic instability, and inhibition of hematopoietic differentiation (By similarity). {ECO:0000250}.
• Pathway: Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.0952

Intolerance Scores

• loftool: 0.885
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.718
• hipred: N
• hipred_score: 0.190
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.356

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myct1

Zebrafish Information Network

• Gene name: myct1a
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Cellular component: nucleoplasm;intracellular membrane-bounded organelle