SLK

STE20 like kinase

Basic information

Region (hg38): 10:103967139-104029233

Links

ENSG00000065613 ∙ NCBI:9748 ∙ OMIM:616563 ∙ HGNC:11088 ∙ Uniprot:Q9H2G2 ∙ 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 SLK gene.

• Inborn genetic diseases (27 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLK 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			26	1	1	28
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	28	2	1

Variants in SLK

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

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

Position	Type	Phenotype	Significance	ClinVar
10-103967800-A-C		not specified	Uncertain significance (Jun 29, 2023)
10-103992590-G-T			Likely benign (Apr 10, 2018)
10-103992985-A-C		not specified	Uncertain significance (Dec 18, 2023)
10-103993122-A-G		not specified	Uncertain significance (Jun 30, 2022)
10-103999201-A-G		not specified	Uncertain significance (Oct 17, 2023)
10-103999291-A-G		not specified	Uncertain significance (Oct 12, 2022)
10-103999312-T-G		not specified	Uncertain significance (Aug 24, 2023)
10-103999911-A-G		not specified	Uncertain significance (Oct 05, 2023)
10-103999943-C-A		not specified	Uncertain significance (Dec 06, 2022)
10-104002250-T-A		not specified	Uncertain significance (Dec 09, 2023)
10-104002277-A-G		not specified	Uncertain significance (Jan 26, 2022)
10-104002335-C-T		not specified	Uncertain significance (Nov 09, 2023)
10-104002385-G-A		not specified	Uncertain significance (Jan 26, 2022)
10-104002575-A-T		not specified	Uncertain significance (Jan 03, 2024)
10-104002592-G-T			Likely pathogenic (Mar 25, 2024)
10-104002671-C-T		not specified	Uncertain significance (Dec 15, 2023)
10-104002682-G-A		not specified	Uncertain significance (Jan 22, 2024)
10-104002739-G-T		not specified	Uncertain significance (Dec 15, 2023)
10-104002785-A-G		not specified	Uncertain significance (Dec 21, 2021)
10-104002880-G-A		not specified	Uncertain significance (May 22, 2023)
10-104002885-G-T			Likely benign (Nov 01, 2022)
10-104002913-G-A		not specified	Uncertain significance (Jun 14, 2022)
10-104002922-C-G		not specified	Uncertain significance (Sep 15, 2021)
10-104002992-T-C		not specified	Uncertain significance (Mar 31, 2022)
10-104003004-A-G		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLK	protein_coding	protein_coding	ENST00000369755	19	62033

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.374	0.626	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.65	442	629	0.703	0.0000318	8266
Missense in Polyphen		131	285.18	0.45935		3692
Synonymous	0.915	196	213	0.920	0.0000103	2146
Loss of Function	5.84	15	66.3	0.226	0.00000367	802

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000282	0.000282
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates apoptosis and actin stress fiber dissolution. {ECO:0000250}.
• Pathway: Oocyte meiosis - Homo sapiens (human);Caspase Cascade in Apoptosis (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.699
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.16

Haploinsufficiency Scores

• pHI: 0.183
• hipred: Y
• hipred_score: 0.706
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.590

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slk
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype

Gene ontology

• Biological process: apoptotic process;signal transduction by protein phosphorylation;regulation of cell migration;stress-activated protein kinase signaling cascade;cytoplasmic microtubule organization;activation of protein kinase activity;regulation of apoptotic process;protein autophosphorylation;regulation of focal adhesion assembly
• Cellular component: cytoplasm;cell leading edge;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;identical protein binding;protein homodimerization activity;cadherin binding