STK40

serine/threonine kinase 40

Basic information

Region (hg38): 1:36339623-36385924

Links

ENSG00000196182 ∙ NCBI:83931 ∙ OMIM:609437 ∙ HGNC:21373 ∙ Uniprot:Q8N2I9 ∙ 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 STK40 gene.

• Inborn genetic diseases (14 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK40 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	2	3
missense			14			14
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	1	2

Variants in STK40

This is a list of pathogenic ClinVar variants found in the STK40 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-36341828-C-T		not specified	Uncertain significance (Jun 03, 2022)
1-36341843-G-T		not specified	Uncertain significance (Sep 20, 2023)
1-36341850-C-T		not specified	Uncertain significance (Mar 31, 2023)
1-36341865-G-T		not specified	Uncertain significance (Dec 02, 2022)
1-36341907-C-G		not specified	Uncertain significance (Feb 22, 2024)
1-36341962-C-T			Benign (Dec 14, 2017)
1-36343900-C-T		not specified	Likely benign (May 18, 2022)
1-36343912-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-36344125-A-G			Benign (Dec 14, 2017)
1-36344136-C-T		not specified	Uncertain significance (Oct 21, 2021)
1-36344261-C-T		not specified	Uncertain significance (Nov 09, 2023)
1-36354370-T-C		not specified	Uncertain significance (Jun 28, 2022)
1-36355316-C-T		not specified	Uncertain significance (Mar 16, 2022)
1-36355338-A-G			Likely benign (Apr 01, 2023)
1-36355429-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-36358242-G-T		not specified	Uncertain significance (Jan 07, 2022)
1-36358250-C-T		not specified	Uncertain significance (Jun 28, 2023)
1-36358276-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-36358330-C-T		not specified	Uncertain significance (Dec 22, 2023)
1-36358341-G-C		not specified	Uncertain significance (Oct 04, 2022)
1-36358747-T-C		not specified	Uncertain significance (Dec 13, 2023)
1-36358768-T-C		not specified	Uncertain significance (Nov 23, 2021)
1-36358769-T-G		not specified	Uncertain significance (Dec 12, 2023)
1-36358774-G-A		not specified	Uncertain significance (Jun 06, 2023)
1-36361292-G-A		not specified	Uncertain significance (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK40	protein_coding	protein_coding	ENST00000373129	10	46273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00376	125730	0	6	125736	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	218	288	0.757	0.0000193	2833
Missense in Polyphen		59	106.23	0.5554		1087
Synonymous	1.18	107	124	0.865	0.00000910	862
Loss of Function	4.03	1	20.9	0.0479	9.72e-7	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a negative regulator of NF-kappa-B and p53- mediated gene transcription. {ECO:0000269|PubMed:13679039}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.171
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.17

Haploinsufficiency Scores

• pHI: 0.288
• hipred: Y
• hipred_score: 0.580
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk40
• Phenotype: respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: respiratory system process;glycogen metabolic process;protein phosphorylation;regulation of gene expression;multicellular organism growth;negative regulation of apoptotic process;regulation of MAPK cascade;lung alveolus development;lung morphogenesis
• Cellular component: nucleoplasm;cytosol
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding