STK31

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

Basic information

Region (hg38): 7:23710203-23832513

Links

ENSG00000196335 ∙ NCBI:56164 ∙ OMIM:605790 ∙ HGNC:11407 ∙ Uniprot:Q9BXU1 ∙ 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 STK31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK31 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			43	8		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	9	0

Variants in STK31

This is a list of pathogenic ClinVar variants found in the STK31 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-23710294-C-A			Likely benign (Jan 01, 2023)
7-23710308-C-A		not specified	Uncertain significance (May 23, 2024)
7-23710308-C-T		not specified	Uncertain significance (Sep 16, 2021)
7-23710311-G-A		not specified	Uncertain significance (Feb 14, 2023)
7-23710323-C-T		not specified	Uncertain significance (Feb 28, 2023)
7-23717488-A-G		not specified	Likely benign (Jul 19, 2023)
7-23717553-G-A		not specified	Uncertain significance (Jun 18, 2024)
7-23727305-G-A		not specified	Uncertain significance (Feb 27, 2023)
7-23729180-T-G		not specified	Uncertain significance (Apr 20, 2024)
7-23735706-A-G		not specified	Uncertain significance (Nov 18, 2022)
7-23735792-A-T		not specified	Uncertain significance (May 17, 2023)
7-23735805-A-G		not specified	Likely benign (Jun 06, 2023)
7-23736909-G-C		not specified	Uncertain significance (Jul 14, 2021)
7-23736935-G-C		not specified	Uncertain significance (Apr 01, 2024)
7-23737007-G-C		not specified	Uncertain significance (Dec 05, 2022)
7-23737046-T-A		not specified	Uncertain significance (Mar 30, 2024)
7-23752718-A-C		not specified	Uncertain significance (Jun 24, 2022)
7-23752751-A-G		not specified	Uncertain significance (Mar 04, 2024)
7-23752763-C-T		not specified	Uncertain significance (Dec 19, 2023)
7-23752784-C-A		not specified	Uncertain significance (Feb 13, 2024)
7-23754322-G-A		not specified	Likely benign (Sep 29, 2023)
7-23754334-C-T			Likely benign (Jan 01, 2023)
7-23754421-A-T		not specified	Uncertain significance (Sep 22, 2022)
7-23762906-C-T		not specified	Uncertain significance (Oct 06, 2022)
7-23769026-G-A		not specified	Uncertain significance (Apr 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK31	protein_coding	protein_coding	ENST00000355870	24	122347

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00662	0.993	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.262	489	506	0.967	0.0000240	6728
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00100	0.000990
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000437	0.000435
Finnish	0.000694	0.000693
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000437	0.000435
South Asian	0.000113	0.0000980
Other	0.000501	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0861

Intolerance Scores

• loftool: 0.780
• rvis_EVS: 1.6
• rvis_percentile_EVS: 95.9

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.375

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.511

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk31
• Phenotype: normal phenotype

Gene ontology

• Biological process: RNA catabolic process;protein phosphorylation;nucleic acid phosphodiester bond hydrolysis
• Cellular component: acrosomal vesicle;nucleus;cytoplasm
• Molecular function: RNA binding;nuclease activity;protein serine/threonine kinase activity;ATP binding