SYMPK

symplekin scaffold protein, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 19:45815409-45863194

Links

ENSG00000125755 ∙ NCBI:8189 ∙ OMIM:602388 ∙ HGNC:22935 ∙ Uniprot:Q92797 ∙ 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 SYMPK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYMPK 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				3		3
missense			49	1	1	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	4	1

Variants in SYMPK

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

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

Position	Type	Phenotype	Significance	ClinVar
19-45815640-G-A		not specified	Uncertain significance (Dec 21, 2023)
19-45815643-C-T		not specified	Likely benign (Apr 08, 2024)
19-45815648-G-C		not specified	Uncertain significance (Dec 17, 2023)
19-45815685-C-T		not specified	Uncertain significance (Jun 10, 2024)
19-45815688-C-G		not specified	Uncertain significance (Mar 17, 2023)
19-45815875-A-G			Likely benign (Mar 01, 2023)
19-45815917-C-A		not specified	Uncertain significance (Oct 29, 2021)
19-45815960-T-C		not specified	Uncertain significance (Sep 17, 2021)
19-45815987-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-45815988-G-A		not specified	Uncertain significance (Dec 19, 2023)
19-45816018-G-T		not specified	Uncertain significance (Mar 02, 2023)
19-45816029-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-45816050-C-A		not specified	Uncertain significance (Feb 15, 2023)
19-45816146-G-A		not specified	Uncertain significance (Apr 18, 2023)
19-45816181-A-C		not specified	Uncertain significance (Dec 15, 2022)
19-45816493-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-45816824-G-A		not specified	Uncertain significance (Sep 27, 2022)
19-45817976-G-A		not specified	Uncertain significance (Feb 23, 2023)
19-45822816-T-C		not specified	Uncertain significance (Jun 26, 2023)
19-45823397-A-G		not specified	Uncertain significance (Nov 30, 2021)
19-45825259-T-A		not specified	Uncertain significance (Dec 13, 2023)
19-45826258-G-A		not specified	Uncertain significance (Oct 26, 2023)
19-45826318-C-T		not specified	Uncertain significance (Jun 02, 2024)
19-45826343-G-A		not specified	Uncertain significance (Jul 14, 2022)
19-45827542-G-C		not specified	Uncertain significance (Jun 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYMPK	protein_coding	protein_coding	ENST00000245934	26	47881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000194	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.86	543	765	0.710	0.0000474	8147
Missense in Polyphen		87	218.27	0.3986		2298
Synonymous	-1.09	355	330	1.08	0.0000212	2622
Loss of Function	6.50	5	58.8	0.0851	0.00000301	679

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000535	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000103	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3'-end processing. Specific component of the tight junction (TJ) plaque, but might not be an exclusively junctional component. May have a house- keeping rule. Is involved in pre-mRNA polyadenylation. Enhances SSU72 phosphatase activity. {ECO:0000269|PubMed:16230528, ECO:0000269|PubMed:20861839}.
• Pathway: Tight junction - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Processing of Intronless Pre-mRNAs;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

• loftool: 0.0885
• rvis_EVS: -1.48
• rvis_percentile_EVS: 3.69

Haploinsufficiency Scores

• pHI: 0.113
• hipred: Y
• hipred_score: 0.652
• ghis: 0.647

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.926

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sympk
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;mRNA polyadenylation;mRNA export from nucleus;cell adhesion;mRNA 3'-end processing;negative regulation of protein binding;positive regulation of protein dephosphorylation
• Cellular component: nucleoplasm;cytoplasm;cytosol;cytoskeleton;plasma membrane;bicellular tight junction;nuclear stress granule
• Molecular function: protein binding