STK33

serine/threonine kinase 33

Basic information

Region (hg38): 11:8391868-8594289

Links

ENSG00000130413 ∙ NCBI:65975 ∙ OMIM:607670 ∙ HGNC:14568 ∙ Uniprot:Q9BYT3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 93	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	34155512

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STK33 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK33 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			33	3		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	4	0

Variants in STK33

This is a list of pathogenic ClinVar variants found in the STK33 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-8392529-C-G		not specified	Uncertain significance (Aug 16, 2021)
11-8392539-C-T		not specified	Uncertain significance (Nov 29, 2023)
11-8392592-G-T		not specified	Uncertain significance (Jul 09, 2021)
11-8392647-T-C		not specified	Uncertain significance (Mar 04, 2024)
11-8392657-C-G		not specified	Uncertain significance (Jun 29, 2022)
11-8392667-T-C		not specified	Uncertain significance (Dec 12, 2023)
11-8413533-C-G		not specified	Uncertain significance (Sep 26, 2023)
11-8413553-T-G		not specified	Conflicting classifications of pathogenicity (Jul 01, 2022)
11-8413583-G-A		not specified	Uncertain significance (Aug 21, 2023)
11-8413583-G-C		not specified	Uncertain significance (Jan 11, 2023)
11-8413601-G-A		not specified	Uncertain significance (Dec 26, 2023)
11-8413603-TG-T		Spermatogenic failure 93	Pathogenic (Oct 25, 2024)
11-8413610-T-C		not specified	Uncertain significance (Aug 09, 2021)
11-8413616-A-T		not specified	Likely benign (Feb 28, 2024)
11-8413628-T-C		not specified	Uncertain significance (Aug 02, 2021)
11-8435535-T-C		not specified	Uncertain significance (Jun 13, 2022)
11-8435544-G-C		not specified	Uncertain significance (Dec 03, 2021)
11-8436118-A-C		Neoplasm of the pancreas	Likely pathogenic (May 13, 2016)
11-8436125-G-A		not specified	Uncertain significance (Mar 24, 2023)
11-8440691-C-T		not specified	Likely benign (Sep 01, 2021)
11-8440728-G-C		not specified	Uncertain significance (Mar 07, 2023)
11-8452887-G-A		not specified	Uncertain significance (Apr 01, 2024)
11-8452889-T-G		not specified	Uncertain significance (Feb 05, 2024)
11-8454746-T-G		not specified	Uncertain significance (Mar 01, 2024)
11-8454778-A-G		not specified	Likely benign (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK33	protein_coding	protein_coding	ENST00000447869	12	202419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000217	0.977	125708	0	39	125747	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.490	233	255	0.914	0.0000123	3393
Missense in Polyphen		45	65.922	0.68262		897
Synonymous	-1.18	104	89.8	1.16	0.00000484	900
Loss of Function	2.09	13	24.1	0.540	0.00000111	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000216
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.00	0.00
Finnish	0.0000945	0.0000924
European (Non-Finnish)	0.000182	0.000176
Middle Eastern	0.00	0.00
South Asian	0.000358	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine protein kinase which phosphorylates VIME. May play a specific role in the dynamic behavior of the intermediate filament cytoskeleton by phosphorylation of VIME (By similarity). Not essential for the survival of KRAS-dependent AML cell lines. {ECO:0000250, ECO:0000269|PubMed:21742770}.

Recessive Scores

• pRec: 0.0835

Intolerance Scores

• loftool: 0.878
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.69

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.243
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.616

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk33

Gene ontology

• Biological process: signal transduction in response to DNA damage;mitotic DNA damage checkpoint;protein autophosphorylation
• Cellular component: nucleus;cytoplasm;perinuclear region of cytoplasm
• Molecular function: protein serine/threonine kinase activity;ATP binding