RPS6KL1

ribosomal protein S6 kinase like 1, the group of AGC family kinases

Basic information

Region (hg38): 14:74903951-74923302

Links

ENSG00000198208 ∙ NCBI:83694 ∙ ∙ HGNC:20222 ∙ Uniprot:Q9Y6S9 ∙ 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 RPS6KL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS6KL1 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						0
missense			36	5		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	5	0

Variants in RPS6KL1

This is a list of pathogenic ClinVar variants found in the RPS6KL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-74907022-C-G		not specified	Uncertain significance (Dec 27, 2023)
14-74907089-C-T		not specified	Uncertain significance (Jan 16, 2024)
14-74907091-T-C		not specified	Likely benign (Jan 19, 2022)
14-74907445-A-G		not specified	Uncertain significance (May 02, 2024)
14-74907460-C-T		not specified	Uncertain significance (Mar 01, 2024)
14-74907461-G-A		not specified	Uncertain significance (Apr 07, 2023)
14-74907473-C-T		not specified	Uncertain significance (Feb 28, 2024)
14-74907493-T-C		not specified	Uncertain significance (May 20, 2024)
14-74907529-G-T		not specified	Uncertain significance (Oct 12, 2022)
14-74907530-C-A		not specified	Uncertain significance (Oct 12, 2022)
14-74908908-G-A		not specified	Uncertain significance (Oct 25, 2023)
14-74909115-A-G		not specified	Uncertain significance (Oct 12, 2021)
14-74909567-C-T		not specified	Likely benign (May 05, 2023)
14-74909576-G-C		not specified	Uncertain significance (Oct 25, 2023)
14-74909582-G-A		not specified	Uncertain significance (Feb 03, 2022)
14-74909626-A-G		not specified	Likely benign (Nov 08, 2022)
14-74909654-C-T		not specified	Uncertain significance (Jan 17, 2023)
14-74909741-C-G		not specified	Uncertain significance (Jul 13, 2022)
14-74909743-C-T		not specified	Uncertain significance (Dec 06, 2022)
14-74909756-C-T		not specified	Uncertain significance (May 13, 2024)
14-74909785-C-T		not specified	Likely benign (Oct 29, 2021)
14-74909857-G-A		not specified	Uncertain significance (Oct 26, 2022)
14-74909866-G-A		not specified	Likely benign (Apr 20, 2024)
14-74909875-G-C		not specified	Uncertain significance (Oct 20, 2023)
14-74909891-C-T		not specified	Uncertain significance (Aug 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS6KL1	protein_coding	protein_coding	ENST00000555647	10	19443

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-7	0.948	125637	2	109	125748	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.610	310	342	0.907	0.0000218	3494
Missense in Polyphen		113	128.22	0.88127		1356
Synonymous	0.897	134	148	0.906	0.00000971	1185
Loss of Function	1.91	15	25.4	0.591	0.00000141	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000415	0.000413
Ashkenazi Jewish	0.000119	0.0000992
East Asian	0.000989	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000216	0.000193
Middle Eastern	0.000989	0.000979
South Asian	0.00212	0.00183
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.05
• rvis_percentile_EVS: 57.48

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.229
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.253

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps6kl1
• Phenotype: hematopoietic system phenotype

Gene ontology

• Biological process: protein phosphorylation
• Cellular component: ribosome
• Molecular function: protein serine/threonine kinase activity;ATP binding