RSKR

ribosomal protein S6 kinase related

Basic information

Region (hg38): 17:28455751-28614197

Links

ENSG00000167524 ∙ NCBI:124923 ∙ ∙ HGNC:26314 ∙ Uniprot:Q96LW2 ∙ 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 RSKR gene.

• T-cell immunodeficiency, congenital alopecia, and nail dystrophy (494 variants)
• not provided (248 variants)
• Inborn genetic diseases (153 variants)
• Cone-rod dystrophy (38 variants)
• not specified (27 variants)
• T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant (9 variants)
• Glycosylphosphatidylinositol biosynthesis defect 18 (6 variants)
• T-cell immunodeficiency, congenital alopecia, and nail dystrophy;T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant (6 variants)
• FOXN1-related condition (4 variants)
• Idiopathic CD4 lymphocytopenia (4 variants)
• See cases (3 variants)
• T-cell lymphopenia, infantile, with or without nail dystrophy, autosomal dominant;T-cell immunodeficiency, congenital alopecia, and nail dystrophy (2 variants)
• UNC119-related condition (2 variants)
• Cone-rod dystrophy 24 (1 variants)
• Relative macrocephaly;Severe T-cell immunodeficiency;Aplasia of the thymus (1 variants)
• T-CELL LYMPHOPENIA, INFANTILE, WITHOUT NAIL DYSTROPHY, AUTOSOMAL DOMINANT (1 variants)
• T-lymphocyte deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSKR 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	31	16	485	259	46	837
Total	31	16	494	259	46

Highest pathogenic variant AF is 0.00000657

Variants in RSKR

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

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

Position	Type	Phenotype	Significance	ClinVar
17-28473725-T-C		not specified	Uncertain significance (Apr 04, 2023)
17-28473731-G-A		not specified	Uncertain significance (Mar 31, 2022)
17-28473803-G-A		not specified	Likely benign (Dec 06, 2022)
17-28489337-T-C		not specified	Uncertain significance (Aug 08, 2023)
17-28490517-G-A		not specified	Uncertain significance (Feb 01, 2023)
17-28490581-G-A		not specified	Uncertain significance (Sep 26, 2022)
17-28490723-G-C		not specified	Uncertain significance (Nov 07, 2023)
17-28490742-T-C		not specified	Uncertain significance (Sep 22, 2022)
17-28490851-C-A		not specified	Uncertain significance (Sep 22, 2023)
17-28490877-C-A		not specified	Uncertain significance (Jul 05, 2023)
17-28491461-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-28491469-T-G		not specified	Uncertain significance (Oct 27, 2022)
17-28491752-G-A		not specified	Uncertain significance (Jul 15, 2021)
17-28491764-G-A		not specified	Uncertain significance (Oct 27, 2022)
17-28491800-A-G		not specified	Uncertain significance (Sep 16, 2021)
17-28493575-C-T		not specified	Uncertain significance (Feb 10, 2022)
17-28493585-T-C		not specified	Uncertain significance (Dec 21, 2022)
17-28493596-G-C		not specified	Uncertain significance (Jul 14, 2021)
17-28493644-G-A		not specified	Uncertain significance (Jun 16, 2023)
17-28493651-G-A		not specified	Likely benign (Aug 02, 2023)
17-28494031-G-A		not specified	Uncertain significance (Jan 17, 2024)
17-28494099-G-T		not specified	Uncertain significance (Oct 26, 2021)
17-28494457-C-T		not specified	Uncertain significance (Apr 13, 2022)
17-28495672-G-A			Uncertain significance (-)
17-28495716-C-T			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RSKR	protein_coding	protein_coding	ENST00000301037	12	6237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.28e-10	0.681	124651	16	1081	125748	0.00437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.269	220	232	0.950	0.0000126	2660
Missense in Polyphen		75	76.21	0.98413		980
Synonymous	0.441	81	86.2	0.940	0.00000449	819
Loss of Function	1.41	18	25.7	0.701	0.00000144	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00134	0.00133
Ashkenazi Jewish	0.00133	0.00129
East Asian	0.000221	0.000217
Finnish	0.0316	0.0254
European (Non-Finnish)	0.00417	0.00410
Middle Eastern	0.000221	0.000217
South Asian	0.000350	0.000327
Other	0.00534	0.00506

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.483

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: BC030499