SHISA5

shisa family member 5, the group of Shisa family members

Basic information

Region (hg38): 3:48467798-48504826

Links

ENSG00000164054 ∙ NCBI:51246 ∙ OMIM:607290 ∙ HGNC:30376 ∙ Uniprot:Q8N114 ∙ 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 SHISA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHISA5 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in SHISA5

This is a list of pathogenic ClinVar variants found in the SHISA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-48469138-G-A		not specified	Uncertain significance (Jan 18, 2025)
3-48469175-C-T		not specified	Uncertain significance (Jul 26, 2024)
3-48469373-C-T		not specified	Uncertain significance (Jan 08, 2025)
3-48469384-G-A		not specified	Uncertain significance (Aug 09, 2021)
3-48469427-T-C		not specified	Uncertain significance (Oct 30, 2023)
3-48469432-T-C		not specified	Uncertain significance (Jan 03, 2022)
3-48469507-G-A		not specified	Uncertain significance (May 03, 2023)
3-48469532-G-A		not specified	Uncertain significance (Jun 18, 2021)
3-48469544-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-48469731-G-A		not specified	Uncertain significance (Feb 20, 2025)
3-48469739-C-T		not specified	Uncertain significance (Dec 28, 2022)
3-48469745-G-A		not specified	Likely benign (Mar 07, 2024)
3-48469755-G-T		not specified	Uncertain significance (Dec 27, 2023)
3-48479217-C-T		not specified	Uncertain significance (Jul 09, 2021)
3-48479244-C-T		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHISA5	protein_coding	protein_coding	ENST00000296444	6	33063

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000111	0.359	125706	0	36	125742	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.285	141	151	0.935	0.00000930	1509
Missense in Polyphen		65	64.126	1.0136		638
Synonymous	-0.292	66	63.1	1.05	0.00000433	506
Loss of Function	0.467	10	11.7	0.853	6.82e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000274
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000197	0.000193
Middle Eastern	0.00	0.00
South Asian	0.000264	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can induce apoptosis in a caspase-dependent manner and plays a role in p53/TP53-dependent apoptosis. {ECO:0000269|PubMed:12135983}.
• Pathway: p53 signaling pathway - Homo sapiens (human);miRNA regulation of p53 pathway in prostate cancer;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.0961

Intolerance Scores

• loftool: 0.824
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.146
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.167

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shisa5
• Phenotype: normal phenotype

Gene ontology

• Biological process: intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;positive regulation of I-kappaB kinase/NF-kappaB signaling;post-translational protein modification;cellular protein metabolic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;integral component of membrane;nuclear membrane
• Molecular function: protein binding