SRPK3

SRSF protein kinase 3

Basic information

Region (hg38): X:153776412-153785732

Previous symbols: [ "STK23" ]

Links

ENSG00000184343 ∙ NCBI:26576 ∙ OMIM:301002 ∙ HGNC:11402 ∙ Uniprot:Q9UPE1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked 114	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	39073169

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SRPK3 gene.

• Congenital myopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRPK3 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				4	2	6
missense			62	2	1	65
nonsense						0
start loss						0
frameshift	1		3			4
inframe indel				1		1
splice donor/acceptor (+/-2bp)			3			3
splice region			1		1	2
non coding					1	1
Total	1	0	68	7	4

Variants in SRPK3

This is a list of pathogenic ClinVar variants found in the SRPK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-153776424-C-T		not specified	Uncertain significance (Nov 13, 2023)
X-153776443-C-T			Uncertain significance (Sep 01, 2018)
X-153776914-G-A		not specified	Likely benign (Aug 05, 2024)
X-153776924-T-C		not specified	Uncertain significance (Dec 28, 2023)
X-153776929-C-T		not specified	Uncertain significance (Jun 29, 2023)
X-153776930-G-A		not specified	Uncertain significance (Apr 19, 2024)
X-153776964-G-A			Benign (Mar 26, 2021)
X-153776977-G-A		not specified	Uncertain significance (Jul 06, 2024)
X-153777228-G-A		not specified	Uncertain significance (Dec 24, 2024)
X-153777231-G-A		not specified	Uncertain significance (May 28, 2024)
X-153777236-G-C		not specified	Uncertain significance (Mar 15, 2024)
X-153777258-C-G		not specified	Uncertain significance (Oct 29, 2021)
X-153777273-G-A		not specified	Uncertain significance (Oct 08, 2024)
X-153777290-C-T			Benign (Oct 22, 2018)
X-153777294-G-A		not specified	Uncertain significance (Jan 29, 2024)
X-153777318-C-G		not specified	Uncertain significance (Jun 13, 2022)
X-153777382-T-C			Uncertain significance (Mar 01, 2024)
X-153777541-A-G		not specified	Uncertain significance (May 22, 2024)
X-153777624-G-A		not specified	Uncertain significance (Aug 02, 2021)
X-153777636-G-A		not specified	Uncertain significance (Jun 07, 2024)
X-153777983-A-G		not specified	Uncertain significance (Nov 13, 2024)
X-153777995-T-A		not specified	Uncertain significance (Sep 03, 2024)
X-153778049-A-G		not specified	Uncertain significance (Aug 04, 2021)
X-153778052-C-A		not specified	Uncertain significance (Aug 07, 2023)
X-153778057-A-G		not specified	Uncertain significance (Dec 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRPK3	protein_coding	protein_coding	ENST00000370101	15	9321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.292	0.707	125557	6	10	125573	0.0000637

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0307	262	263	0.995	0.0000242	3664
Missense in Polyphen		73	78.694	0.92764		1111
Synonymous	-3.23	164	119	1.38	0.0000117	1152
Loss of Function	3.26	5	21.2	0.235	0.00000151	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000558	0.000455
Ashkenazi Jewish	0.000135	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000501	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000108	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/arginine-rich protein-specific kinase which specifically phosphorylates its substrates at serine residues located in regions rich in arginine/serine dipeptides, known as RS domains. Phosphorylates the SR splicing factor SRSF1 and the lamin-B receptor (LBR) in vitro. Required for normal muscle development (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.652
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.82

Haploinsufficiency Scores

• pHI: 0.229
• hipred: Y
• hipred_score: 0.532
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.256

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srpk3
• Phenotype: muscle phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: spliceosomal complex assembly;protein phosphorylation;skeletal muscle tissue development;regulation of gene expression;cell differentiation;intracellular signal transduction;regulation of mRNA processing;muscle tissue development
• Cellular component: cellular_component;nucleus;cytoplasm
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding