STK17A

protein-coding

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

Gene summary

This gene is a member of the DAP kinase-related apoptosis-inducing protein kinase family and encodes an autophosphorylated nuclear protein with a protein kinase domain. The protein has apoptosis-inducing activity. [provided by RefSeq, Jul 2008]

MANE transcript

NM_004760.3

Inheritance

—

ClinVar variants

U:48B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr7:43,582,758-43,650,713

External References & Databases

Ensembl (ENSG00000164543)

Transcript & Mutation Effects

hg38 • Region Span ~68.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to STK17A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 50

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004760.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			48 clinvar	3 clinvar		51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	3	1	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004760.3	RefSeq	NP_004751.2	7	MANE Select
ENST00000319357.6	Ensembl	ENSP00000319192.5	7	MANE Select
ENST00000648544.1	Ensembl	ENSP00000497301.1	7	Standard
ENST00000869874.1	Ensembl	ENSP00000539933.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
apoptotic process
intracellular signal transduction
positive regulation of apoptotic process
positive regulation of fibroblast apoptotic process

Molecular Function

protein serine/threonine kinase activity
ATP binding

Cellular Component

nucleus
plasma membrane
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000319357
Coding exons: 7
Length: 44029
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 62
Defined: 125740
p: 0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.466	183	202	0.908	0.00000943	2679
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00046	0.00046	rare
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.00033	0.00033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.707

Gene Damage Prediction

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