STK32B

protein-coding

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

Gene summary

This gene encodes a serine-threonine protein kinase. Serine-threonine kinases transfer phosphate molecules to the oxygen atoms of serine and threonine. A genomic deletion affecting this gene has been associated with Ellis-van Creveld syndrome, an autosomal recessive skeletal dysplasia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

MANE transcript

NM_018401.3

Inheritance

—

ClinVar variants

U:85B:8

Top phenotype

Long QT syndrome

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr4:5,051,480-5,500,994

External References & Databases

Ensembl (ENSG00000152953)

Transcript & Mutation Effects

hg38 • Region Span ~449.5 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 STK32B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 10

Long QT syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018401.3. 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	3 clinvar	3 clinvar	7
missense			82 clinvar	2 clinvar		84
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	85	5	3	93

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018401.3	RefSeq	NP_060871.1	12	MANE Select
ENST00000282908.10	Ensembl	ENSP00000282908.5	12	MANE Select
NM_001306082.2	RefSeq	NP_001293011.1	10	Standard
NM_001345969.2	RefSeq	NP_001332898.1	11	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: ENST00000282908
Coding exons: 12
Length: 449557
Individuals with no LoFs: 125713
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 125748
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.984	286	243	1.18	0.0000141	2755
Missense (PolyPhen)		108	102.38	1.0549		1173
Synonymous	-2.20	127	99.1	1.28	0.00000628	743
Loss of Function	1.57	15	23.1	0.648	0.00000115	267

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00065	0.00060	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00013	0.00011	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.717
RVIS EVS: -0.64
RVIS percentile EVS: 16.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.360

Gene Damage Prediction

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