STK31

protein-coding

serine/threonine kinase 31, the group of Tudor domain containing

Gene summary

This gene is similar to a mouse gene that encodes a putative protein kinase with a tudor domain, and shows testis-specific expression. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

MANE transcript

NM_031414.5

Inheritance

—

ClinVar variants

U:131B:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr7:23,710,203-23,832,513

External References & Databases

Ensembl (ENSG00000196335)

Transcript & Mutation Effects

hg38 • Region Span ~122.3 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 STK31 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 138

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031414.5. 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			3 clinvar	1 clinvar		4
missense			127 clinvar	16 clinvar		143
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	131	18	0	149

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031414.5	RefSeq	NP_113602.2	24	MANE Select
ENST00000355870.8	Ensembl	ENSP00000348132.3	24	MANE Select
NM_001260504.2	RefSeq	NP_001247433.1	23	Standard
NM_001260505.2	RefSeq	NP_001247434.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

RNA catabolic process
protein phosphorylation
nucleic acid phosphodiester bond hydrolysis

Molecular Function

RNA binding
nuclease activity
protein serine/threonine kinase activity
ATP binding

Cellular Component

acrosomal vesicle
nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355870
Coding exons: 24
Length: 122347
Individuals with no LoFs: 125673
Homozygous LoFs: 0
Heterozygous LoFs: 75
Defined: 125748
p: 0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.262	489	506	0.967	0.0000240	6728
Missense (PolyPhen)		78	140.11	0.55669		1950
Synonymous	-1.05	195	177	1.10	0.00000887	1804
Loss of Function	4.94	15	54.3	0.276	0.00000254	743

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.00056	0.00055	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00044	0.00044	rare
Finnish	0.00069	0.00069	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00011	0.000098	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0861

Intolerance Scores

LoFtool: 0.780
RVIS EVS: 1.6
RVIS percentile EVS: 95.9

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.511

Gene Damage Prediction

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