PKMYT1

protein kinase, membrane associated tyrosine/threonine 1, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 16:2968023-2980479

Links

ENSG00000127564 ∙ NCBI:9088 ∙ OMIM:602474 ∙ HGNC:29650 ∙ Uniprot:Q99640 ∙ 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 PKMYT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKMYT1 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			43	1		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	1	1

Variants in PKMYT1

This is a list of pathogenic ClinVar variants found in the PKMYT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2969682-T-A		not specified	Uncertain significance (Oct 26, 2021)
16-2969739-A-G		not specified	Uncertain significance (Oct 03, 2022)
16-2969768-G-A		not specified	Uncertain significance (Dec 01, 2022)
16-2969783-G-A		not specified	Uncertain significance (May 15, 2024)
16-2971202-C-T		not specified	Uncertain significance (Jan 09, 2024)
16-2971216-G-C		not specified	Uncertain significance (Oct 27, 2022)
16-2971222-G-T		not specified	Uncertain significance (Dec 21, 2023)
16-2971330-C-T		not specified	Uncertain significance (Oct 02, 2023)
16-2971360-T-C		not specified	Uncertain significance (Dec 13, 2023)
16-2971373-C-T		not specified	Uncertain significance (Jun 29, 2023)
16-2971566-C-T		not specified	Uncertain significance (Apr 04, 2023)
16-2971607-G-T		not specified	Uncertain significance (Oct 12, 2021)
16-2971613-C-T		not specified	Uncertain significance (Jul 22, 2022)
16-2971628-C-T		not specified	Uncertain significance (Apr 18, 2023)
16-2971650-G-A		not specified	Uncertain significance (Oct 05, 2023)
16-2971673-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-2971677-G-A		not specified	Uncertain significance (Mar 15, 2024)
16-2971749-G-A		not specified	Uncertain significance (May 07, 2024)
16-2971753-G-A		not specified	Uncertain significance (Feb 23, 2023)
16-2971757-G-A		not specified	Uncertain significance (Jun 02, 2023)
16-2971764-C-T		not specified	Uncertain significance (Aug 15, 2023)
16-2971793-C-T		not specified	Uncertain significance (Sep 16, 2021)
16-2971794-G-A		not specified	Uncertain significance (Jan 02, 2024)
16-2971820-C-T		not specified	Uncertain significance (Feb 01, 2023)
16-2971867-C-T		not specified	Likely benign (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKMYT1	protein_coding	protein_coding	ENST00000262300	8	12516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.219	0.781	125236	0	12	125248	0.0000479

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0740	286	290	0.988	0.0000187	3104
Missense in Polyphen		49	68.258	0.71786		785
Synonymous	-0.625	134	125	1.07	0.00000760	1097
Loss of Function	3.13	5	20.2	0.248	9.66e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000225	0.000215
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000697	0.0000620
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a negative regulator of entry into mitosis (G2 to M transition) by phosphorylation of the CDK1 kinase specifically when CDK1 is complexed to cyclins. Mediates phosphorylation of CDK1 predominantly on 'Thr-14'. Also involved in Golgi fragmentation. May be involved in phosphorylation of CDK1 on 'Tyr-15' to a lesser degree, however tyrosine kinase activity is unclear and may be indirect. May be a downstream target of Notch signaling pathway during eye development. {ECO:0000269|PubMed:10373560, ECO:0000269|PubMed:9001210}.
• Pathway: Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Cell Cycle;G2/M DNA replication checkpoint;G2/M Checkpoints;Polo-like kinase mediated events;Cell Cycle Checkpoints;Cyclin A/B1/B2 associated events during G2/M transition;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.532
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.51

Haploinsufficiency Scores

• pHI: 0.361
• hipred: Y
• hipred_score: 0.770
• ghis: 0.595

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.967

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pkmyt1

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;G2/M transition of mitotic cell cycle;mitotic cell cycle;protein phosphorylation;regulation of mitotic nuclear division;negative regulation of phosphatase activity;meiotic cell cycle
• Cellular component: Golgi membrane;nucleus;nucleoplasm;nucleolus;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;cytosol;membrane
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;kinase activity;metal ion binding