SHISA7

shisa family member 7, the group of Shisa family members

Basic information

Region (hg38): 19:55428740-55443300

Links

ENSG00000187902 ∙ NCBI:729956 ∙ OMIM:617328 ∙ HGNC:35409 ∙ Uniprot:A6NL88 ∙ 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 SHISA7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHISA7 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			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	0

Variants in SHISA7

This is a list of pathogenic ClinVar variants found in the SHISA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55433272-G-C		not specified	Uncertain significance (Nov 09, 2022)
19-55433310-G-C		not specified	Uncertain significance (Sep 16, 2021)
19-55433312-C-A		not specified	Uncertain significance (Jun 22, 2024)
19-55433323-C-A		not specified	Uncertain significance (Nov 22, 2024)
19-55433323-C-T		not specified	Uncertain significance (Oct 20, 2023)
19-55433332-C-A		not specified	Uncertain significance (Jan 27, 2022)
19-55433359-A-G		not specified	Likely benign (Feb 08, 2025)
19-55433374-C-T		not specified	Uncertain significance (Jan 29, 2024)
19-55433400-G-C		not specified	Uncertain significance (Jan 21, 2025)
19-55433453-G-T		not specified	Likely benign (Feb 06, 2025)
19-55433454-T-G		not specified	Uncertain significance (Jun 18, 2021)
19-55433518-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-55433559-G-A		not specified	Uncertain significance (Oct 25, 2024)
19-55433560-C-T		not specified	Uncertain significance (Feb 15, 2025)
19-55433580-T-C		not specified	Uncertain significance (Nov 08, 2022)
19-55433615-C-G		not specified	Uncertain significance (Oct 12, 2024)
19-55433656-C-T		not specified	Uncertain significance (Jan 31, 2024)
19-55433665-C-T		not specified	Uncertain significance (Feb 08, 2025)
19-55433697-C-A		not specified	Uncertain significance (Apr 07, 2023)
19-55433721-G-A		not specified	Uncertain significance (Jun 07, 2024)
19-55433742-C-T		not specified	Uncertain significance (Feb 23, 2023)
19-55433752-C-G		not specified	Uncertain significance (Feb 15, 2023)
19-55433760-C-T		not specified	Uncertain significance (Aug 09, 2021)
19-55437664-G-A		not specified	Uncertain significance (Aug 11, 2024)
19-55440623-T-G		not specified	Likely benign (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHISA7	protein_coding	protein_coding	ENST00000376325	4	14124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.854	0.144	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	80	137	0.582	0.00000809	3316
Missense in Polyphen		21	36.671	0.57265		795
Synonymous	0.654	60	66.8	0.898	0.00000406	1286
Loss of Function	2.33	0	6.31	0.00	2.74e-7	135

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: Regulator of long-term synaptic potentiation specifically involved in the formation and retrieval of hippocampus-dependent contextual fear memory. Probably regulates induction and maintenance of long-term potentiation at Schaffer collaterals/CA3-CA1 excitatory synapses by affecting the recruitment of AMPA-type glutamate receptor (AMPAR) at postsynaptic density. {ECO:0000250|UniProtKB:Q8C3Q5}.

Haploinsufficiency Scores

• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shisa7
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: memory;regulation of short-term neuronal synaptic plasticity;regulation of postsynaptic neurotransmitter receptor activity;positive regulation of long-term synaptic potentiation;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 specialization membrane
• Molecular function: ionotropic glutamate receptor binding