SHISA6

shisa family member 6, the group of Shisa family members

Basic information

Region (hg38): 17:11241213-11564063

Links

ENSG00000188803 ∙ NCBI:388336 ∙ OMIM:617327 ∙ HGNC:34491 ∙ Uniprot:Q6ZSJ9 ∙ 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 SHISA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHISA6 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			48			48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	0	0

Variants in SHISA6

This is a list of pathogenic ClinVar variants found in the SHISA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-11241469-C-T		not specified	Uncertain significance (Aug 17, 2022)
17-11241484-C-T		not specified	Uncertain significance (Apr 29, 2024)
17-11241516-A-C		not specified	Uncertain significance (Aug 12, 2021)
17-11241528-A-C		not specified	Uncertain significance (Sep 17, 2021)
17-11241529-G-A		not specified	Uncertain significance (Dec 14, 2023)
17-11241530-T-G		not specified	Uncertain significance (Sep 17, 2021)
17-11241540-G-T		not specified	Uncertain significance (Jul 26, 2024)
17-11241547-T-G		not specified	Uncertain significance (Jul 06, 2021)
17-11241565-G-T		not specified	Uncertain significance (Jul 05, 2023)
17-11241568-G-A		not specified	Uncertain significance (Jan 16, 2024)
17-11241583-G-A		not specified	Uncertain significance (Aug 10, 2021)
17-11241610-G-C		not specified	Uncertain significance (Jul 23, 2024)
17-11241612-G-T		not specified	Uncertain significance (Dec 14, 2021)
17-11241630-G-T		not specified	Uncertain significance (Jan 30, 2024)
17-11241631-C-T		not specified	Uncertain significance (Jan 30, 2024)
17-11241643-G-A		not specified	Uncertain significance (Sep 13, 2023)
17-11241643-G-C		not specified	Uncertain significance (Aug 13, 2021)
17-11241667-C-T		not specified	Uncertain significance (Apr 07, 2023)
17-11241678-A-C		not specified	Uncertain significance (Jun 17, 2024)
17-11241679-G-A		not specified	Uncertain significance (Apr 07, 2023)
17-11241819-C-T		not specified	Uncertain significance (Apr 17, 2024)
17-11241825-G-A		not specified	Uncertain significance (Apr 12, 2022)
17-11241830-G-C		not specified	Uncertain significance (Aug 20, 2024)
17-11241860-G-T		not specified	Uncertain significance (May 23, 2023)
17-11241901-C-G		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHISA6	protein_coding	protein_coding	ENST00000441885	6	322801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.853	0.147	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	197	302	0.652	0.0000192	3488
Missense in Polyphen		120	191.06	0.62806		1939
Synonymous	0.704	122	132	0.922	0.00000900	1158
Loss of Function	3.46	3	19.5	0.154	9.94e-7	235

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in maintenance of high-frequency synaptic transmission at hippocampal CA3-CA1 synapses. Regulates AMPA-type glutamate receptor (AMPAR) immobilization at postsynaptic density keeping the channels in an activated state in the presence of glutamate and preventing synaptic depression. May play a role in self-renewal and differentiation of spermatogonial stem cells by inhibiting canonical Wnt signaling pathway. {ECO:0000250|UniProtKB:Q3UH99}.

Intolerance Scores

• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.89

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shisa6

Gene ontology

• Biological process: spermatogenesis;Wnt signaling pathway;regulation of short-term neuronal synaptic plasticity;negative regulation of canonical Wnt signaling pathway;regulation of postsynaptic neurotransmitter receptor activity;postsynaptic neurotransmitter receptor diffusion trapping;excitatory chemical synaptic transmission;regulation of AMPA glutamate receptor clustering;regulation of AMPA receptor activity
• Cellular component: postsynaptic density;cell junction;AMPA glutamate receptor complex;dendritic spine membrane;synapse;postsynaptic membrane;asymmetric, glutamatergic, excitatory synapse;integral component of postsynaptic density membrane
• Molecular function: PDZ domain binding;ionotropic glutamate receptor binding