STK38L

serine/threonine kinase 38 like, the group of AGC family kinases

Basic information

Region (hg38): 12:27243967-27325959

Links

ENSG00000211455 ∙ NCBI:23012 ∙ OMIM:615836 ∙ HGNC:17848 ∙ Uniprot:Q9Y2H1 ∙ 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 STK38L gene.

• Inborn genetic diseases (7 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK38L 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	2
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	1

Variants in STK38L

This is a list of pathogenic ClinVar variants found in the STK38L region.

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

Position	Type	Phenotype	Significance	ClinVar
12-27297714-C-T		STK38L-related disorder	Benign (Dec 16, 2019)
12-27297738-G-T		STK38L-related disorder	Benign (Jun 26, 2019)
12-27308324-G-GT		STK38L-related disorder	Likely benign (Jun 12, 2019)
12-27308387-C-T		not specified	Uncertain significance (May 30, 2023)
12-27312632-T-G		not specified	Uncertain significance (Jan 23, 2023)
12-27314576-C-T		not specified	Uncertain significance (Nov 17, 2022)
12-27315003-AT-A		STK38L-related disorder	Likely benign (Jul 16, 2019)
12-27315298-A-G		not specified	Uncertain significance (Dec 27, 2023)
12-27317437-G-A		not specified	Uncertain significance (Jun 01, 2023)
12-27319357-G-C		not specified	Uncertain significance (Aug 17, 2021)
12-27319396-T-C		not specified	Uncertain significance (Nov 09, 2021)
12-27319419-A-G		not specified	Uncertain significance (Nov 17, 2022)
12-27322413-A-G			Likely benign (Nov 27, 2017)
12-27322435-A-G		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STK38L	protein_coding	protein_coding	ENST00000389032	13	81992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.934	0.0657	125720	0	15	125735	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.94	117	247	0.473	0.0000124	3085
Missense in Polyphen		31	103.26	0.30021		1287
Synonymous	1.74	60	79.8	0.752	0.00000395	795
Loss of Function	4.03	4	26.3	0.152	0.00000126	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000596	0.0000596
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of structural processes in differentiating and mature neuronal cells. {ECO:0000250, ECO:0000269|PubMed:15037617, ECO:0000269|PubMed:15067004}.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.562
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.728
• hipred: Y
• hipred_score: 0.768
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stk38l
• 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)

Gene ontology

• Biological process: protein phosphorylation;peptidyl-serine phosphorylation;intracellular signal transduction;regulation of cellular component organization
• Cellular component: cytoplasm;cytosol;actin cytoskeleton;membrane
• Molecular function: magnesium ion binding;actin binding;protein serine/threonine kinase activity;protein binding;ATP binding