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RPS6KC1

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

Basic information

Region (hg38): 1:213051232-213274774

Links

ENSG00000136643NCBI:26750OMIM:617517HGNC:10439Uniprot:Q96S38AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
6
clinvar
43
missense
91
clinvar
6
clinvar
7
clinvar
104
nonsense
1
clinvar
1
start loss
0
frameshift
3
clinvar
3
inframe indel
0
splice donor/acceptor (+/-2bp)
2
clinvar
2
clinvar
4
splice region
?
0
non coding
?
12
clinvar
21
clinvar
8
clinvar
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)1941338
1-213051437-G-A Likely benign (Sep 20, 2021)1578508
1-213051446-C-T Likely benign (Dec 02, 2021)1547956
1-213051462-C-A Inborn genetic diseases Uncertain significance (Dec 07, 2021)2265450
1-213051471-C-T Inborn genetic diseases Uncertain significance (Oct 07, 2022)2184907
1-213051475-C-T Inborn genetic diseases Conflicting classifications of pathogenicity (Nov 02, 2023)2459595
1-213051491-A-G Likely benign (Apr 29, 2022)2175137
1-213051517-C-G Likely benign (Apr 08, 2022)1960074
1-213051517-C-T Likely benign (Oct 27, 2023)2726512
1-213051518-C-T Benign (Oct 18, 2022)791830
1-213070988-A-C Benign (Oct 05, 2022)1618446
1-213070988-A-G Benign (Nov 01, 2022)1623900
1-213071003-T-C Uncertain significance (Sep 06, 2022)2075090
1-213071021-A-G Uncertain significance (Apr 12, 2022)2115323
1-213071024-C-A Likely benign (Oct 03, 2022)1159111
1-213071052-T-C Likely benign (Aug 23, 2022)1633506
1-213077690-C-G Likely benign (Aug 10, 2022)1446317
1-213077698-A-C Likely benign (Sep 20, 2022)2030214
1-213077718-G-A Uncertain significance (Mar 14, 2022)2111534
1-213077758-C-T Likely benign (Jul 19, 2022)2015598
1-213077822-T-C Uncertain significance (Jun 08, 2022)2183210
1-213104452-A-G Uncertain significance (Sep 19, 2022)1905468
1-213104455-G-T Likely benign (Sep 13, 2022)2414733
1-213104476-C-A Benign (Dec 11, 2023)1601633
1-213104541-A-C Uncertain significance (Aug 19, 2021)1412378

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS6KC1protein_codingprotein_codingENST00000366960 15223528
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001260.9991257040441257480.000175
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4485195490.9460.00002637027
Missense in Polyphen182226.190.804642892
Synonymous0.05311971980.9950.000009772011
Loss of Function4.321445.40.3080.00000233599

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004680.000450
Ashkenazi Jewish0.000.00
East Asian0.0002180.000217
Finnish0.000.00
European (Non-Finnish)0.0002340.000229
Middle Eastern0.0002180.000217
South Asian0.00009890.0000980
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rps6kc1
Phenotype

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