STK17A

serine/threonine kinase 17a, the group of Death associated protein kinases

Basic information

Region (hg38): 7:43582758-43650713

Links

ENSG00000164543 ∙ NCBI:9263 ∙ OMIM:604726 ∙ HGNC:11395 ∙ Uniprot:Q9UEE5 ∙ 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 STK17A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK17A 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			20	1	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10			10
Total	0	0	30	1	2

Variants in STK17A

This is a list of pathogenic ClinVar variants found in the STK17A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-43583266-G-A		not specified	Uncertain significance (Mar 30, 2024)
7-43583271-G-T		not specified	Uncertain significance (Jan 03, 2024)
7-43583356-A-G		not specified	Uncertain significance (Jan 25, 2024)
7-43583380-T-C		not specified	Uncertain significance (May 16, 2023)
7-43583431-C-T		not specified	Uncertain significance (Aug 21, 2023)
7-43595999-G-A		not specified	Uncertain significance (Dec 08, 2023)
7-43596058-A-G		not specified	Uncertain significance (Jan 26, 2022)
7-43608339-G-A			Benign (May 08, 2018)
7-43608343-G-C		not specified	Uncertain significance (Oct 13, 2023)
7-43608345-T-C		not specified	Uncertain significance (Oct 03, 2022)
7-43608356-G-A		not specified	Uncertain significance (Sep 17, 2021)
7-43608374-C-G		not specified	Uncertain significance (Dec 12, 2023)
7-43608375-G-A		not specified	Likely benign (May 08, 2023)
7-43619643-A-T		not specified	Uncertain significance (Mar 06, 2023)
7-43619645-A-C		not specified	Uncertain significance (Sep 22, 2023)
7-43623585-T-C			Benign (Sep 11, 2018)
7-43623617-T-C		not specified	Uncertain significance (Nov 30, 2022)
7-43623729-A-G		not specified	Uncertain significance (Apr 06, 2023)
7-43623765-A-G		not specified	Uncertain significance (Feb 14, 2023)
7-43623766-T-A		not specified	Uncertain significance (Aug 11, 2022)
7-43623782-T-C		not specified	Uncertain significance (Jan 26, 2023)
7-43624552-C-T		not specified	Uncertain significance (May 23, 2023)
7-43624733-G-C		not specified	Uncertain significance (Aug 02, 2021)
7-43624799-A-C		not specified	Uncertain significance (Mar 01, 2024)
7-43639604-C-T		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK17A	protein_coding	protein_coding	ENST00000319357	7	44029

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0404	0.958	125678	0	62	125740	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.466	183	202	0.908	0.00000943	2679
Missense in Polyphen		61	79.227	0.76994		1052
Synonymous	0.0914	69	70.0	0.986	0.00000339	786
Loss of Function	2.84	6	19.5	0.307	0.00000116	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000419	0.000419
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000462	0.000462
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.000110	0.000109
South Asian	0.000331	0.000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a positive regulator of apoptosis. Also acts as a regulator of cellular reactive oxygen species. {ECO:0000269|PubMed:21489989, ECO:0000269|PubMed:9786912}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.785
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.224
• hipred: N
• hipred_score: 0.478
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.707

Gene Damage Prediction

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

Gene ontology

• Biological process: protein phosphorylation;apoptotic process;intracellular signal transduction;positive regulation of apoptotic process;positive regulation of fibroblast apoptotic process;regulation of reactive oxygen species metabolic process
• Cellular component: nucleus;plasma membrane;nuclear speck
• Molecular function: protein serine/threonine kinase activity;ATP binding