RPS6KC1

ribosomal protein S6 kinase C1, the group of AGC family kinases

Basic information

Region (hg38): 1:213051232-213274774

Links

ENSG00000136643 ∙ NCBI:26750 ∙ OMIM:617517 ∙ HGNC:10439 ∙ Uniprot:Q96S38 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• periventricular leukomalacia (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS6KC1 gene.

• not provided (191 variants)
• Inborn genetic diseases (33 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS6KC1 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				37	6	43
missense			91	6	7	104
nonsense			1			1
start loss						0
frameshift			3			3
inframe indel						0
splice donor/acceptor (+/-2bp)			2		2	4
splice region			2	11	3	16
non coding			12	21	8	41
Total	0	0	109	64	23

Variants in RPS6KC1

This is a list of pathogenic ClinVar variants found in the RPS6KC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-213051424-G-T			Uncertain significance (Aug 09, 2022)
1-213051437-G-A			Likely benign (Sep 20, 2021)
1-213051446-C-T			Likely benign (Dec 02, 2021)
1-213051459-G-A			Uncertain significance (Sep 09, 2023)
1-213051462-C-A		not specified	Uncertain significance (Dec 07, 2021)
1-213051471-C-T		not specified	Uncertain significance (Oct 07, 2022)
1-213051475-C-T		not specified	Conflicting classifications of pathogenicity (Nov 02, 2023)
1-213051480-G-C		not specified	Uncertain significance (Mar 07, 2024)
1-213051490-TA-T			Uncertain significance (Jun 25, 2023)
1-213051491-A-G			Likely benign (Apr 29, 2022)
1-213051517-C-G			Likely benign (Apr 08, 2022)
1-213051517-C-T			Likely benign (Oct 27, 2023)
1-213051518-C-T			Benign (Jan 26, 2024)
1-213070988-A-C			Benign (Jan 22, 2024)
1-213070988-A-G			Benign (Jul 17, 2023)
1-213071003-T-C			Uncertain significance (Sep 06, 2022)
1-213071021-A-G			Uncertain significance (Apr 12, 2022)
1-213071024-C-A			Likely benign (Jan 22, 2024)
1-213071037-A-G			Uncertain significance (Jun 16, 2023)
1-213071052-T-C			Likely benign (Aug 23, 2022)
1-213071058-GATTTT-G			Likely benign (Oct 01, 2023)
1-213077690-C-G			Likely benign (Sep 26, 2023)
1-213077698-A-C			Likely benign (Aug 04, 2023)
1-213077718-G-A			Uncertain significance (Mar 14, 2022)
1-213077744-C-T			Likely benign (Jul 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS6KC1	protein_coding	protein_coding	ENST00000366960	15	223528

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00126	0.999	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.448	519	549	0.946	0.0000263	7027
Missense in Polyphen		182	226.19	0.80464		2892
Synonymous	0.0531	197	198	0.995	0.00000977	2011
Loss of Function	4.32	14	45.4	0.308	0.00000233	599

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000468	0.000450
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000234	0.000229
Middle Eastern	0.000218	0.000217
South Asian	0.0000989	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transmitting sphingosine-1 phosphate (SPP)-mediated signaling into the cell (PubMed:12077123). Plays a role in the recruitment of PRDX3 to early endosomes (PubMed:15750338). {ECO:0000269|PubMed:12077123, ECO:0000269|PubMed:15750338}.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• rvis_EVS: 0.45
• rvis_percentile_EVS: 78.02

Haploinsufficiency Scores

• pHI: 0.121
• hipred: Y
• hipred_score: 0.542
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps6kc1

Gene ontology

• Biological process: protein phosphorylation;signal transduction
• Cellular component: early endosome;membrane
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;phosphatidylinositol binding