STK32C

protein-coding

serine/threonine kinase 32C, the group of AGC family kinases

Gene summary

The protein encoded by this gene is a member of the serine/threonine protein kinase family. It is thought that this family member is functional in brain due to its high expression levels there. DNA methylation differences have been found in this gene in monozygotic twins that are discordant for adolescent depression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

MANE transcript

NM_173575.4

Inheritance

—

ClinVar variants

U:63B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr10:132,207,492-132,331,847

External References & Databases

Ensembl (ENSG00000165752)

Transcript & Mutation Effects

hg38 • Region Span ~124.4 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 STK32C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173575.4. 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		4 clinvar	5
missense			62 clinvar	4 clinvar	1 clinvar	67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	4	5	72

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173575.4	RefSeq	NP_775846.2	12	MANE Select
ENST00000298630.8	Ensembl	ENSP00000298630.3	12	MANE Select
NM_001318878.2	RefSeq	NP_001305807.1	12	Standard
NM_001318879.2	RefSeq	NP_001305808.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

peptidyl-serine phosphorylation
intracellular signal transduction

Molecular Function

protein serine/threonine kinase activity
ATP binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298630
Coding exons: 12
Length: 124356
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125742
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.11	179	278	0.644	0.0000179	3159
Missense (PolyPhen)		39	92.875	0.41992		963
Synonymous	-0.984	138	124	1.11	0.00000910	930
Loss of Function	3.45	6	24.4	0.246	0.00000122	258

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.617
RVIS EVS: -0.36
RVIS percentile EVS: 29.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.749

Gene Damage Prediction

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