SHISA9

shisa family member 9, the group of Shisa family members

Basic information

Region (hg38): 16:12901597-13240416

Links

ENSG00000237515 ∙ NCBI:729993 ∙ OMIM:613346 ∙ HGNC:37231 ∙ Uniprot:B4DS77 ∙ 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 SHISA9 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHISA9 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in SHISA9

This is a list of pathogenic ClinVar variants found in the SHISA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-12902149-C-A		not specified	Uncertain significance (May 11, 2022)
16-12902179-T-G		not specified	Uncertain significance (Apr 07, 2023)
16-12902182-C-G		not specified	Likely benign (Apr 07, 2023)
16-12902249-A-G		not specified	Uncertain significance (May 09, 2023)
16-12902269-C-G		not specified	Uncertain significance (May 16, 2022)
16-12902346-C-G		not specified	Uncertain significance (Mar 22, 2023)
16-12902390-C-T		not specified	Uncertain significance (Jan 04, 2022)
16-12902470-G-A		not specified	Uncertain significance (Feb 17, 2022)
16-12916714-A-T		not specified	Uncertain significance (Jul 17, 2023)
16-12916716-G-A		not specified	Uncertain significance (Jul 14, 2021)
16-12916734-C-A		not specified	Uncertain significance (Dec 15, 2023)
16-12916757-C-G		not specified	Uncertain significance (Sep 16, 2021)
16-12916758-G-A		not specified	Uncertain significance (Mar 07, 2023)
16-13203423-A-G		not specified	Uncertain significance (Aug 13, 2021)
16-13203478-A-G		not specified	Uncertain significance (Jul 25, 2023)
16-13213280-C-T		not specified	Uncertain significance (Feb 14, 2023)
16-13235057-C-G		not specified	Likely benign (Aug 21, 2023)
16-13235061-G-C		not specified	Uncertain significance (Mar 29, 2022)
16-13235066-G-C		not specified	Uncertain significance (Jan 20, 2023)
16-13235154-C-A		not specified	Uncertain significance (Feb 27, 2024)
16-13235161-G-A		not specified	Uncertain significance (Jan 10, 2022)
16-13235203-C-T		not specified	Uncertain significance (Jul 29, 2023)
16-13235225-C-T		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHISA9	protein_coding	protein_coding	ENST00000424107	5	338796

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.873	0.127	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	164	242	0.677	0.0000129	2754
Missense in Polyphen		49	96.987	0.50522		1102
Synonymous	0.725	96	105	0.910	0.00000597	864
Loss of Function	3.18	2	15.5	0.129	8.23e-7	176

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 short-term neuronal synaptic plasticity in the dentate gyrus. Associates with AMPA receptors (ionotropic glutamate receptors) in synaptic spines and promotes AMPA receptor desensitization at excitatory synapses (By similarity). {ECO:0000250}.

Haploinsufficiency Scores

• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Shisa9
• 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)

Gene ontology

• Biological process: regulation of short-term neuronal synaptic plasticity;regulation of postsynaptic neurotransmitter receptor activity;regulation of AMPA receptor activity
• Cellular component: ionotropic glutamate receptor complex;postsynaptic density;cell junction;AMPA glutamate receptor complex;dendritic spine membrane;synapse;postsynaptic membrane;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: PDZ domain binding