SHISA3

shisa family member 3, the group of Shisa family members

Basic information

Region (hg38): 4:42397487-42402487

Links

ENSG00000178343 ∙ NCBI:152573 ∙ OMIM:617325 ∙ HGNC:25159 ∙ Uniprot:A0PJX4 ∙ 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 SHISA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHISA3 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			18	1		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	18	1	0

Variants in SHISA3

This is a list of pathogenic ClinVar variants found in the SHISA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-42398073-C-A		not specified	Uncertain significance (Jan 18, 2022)
4-42398111-G-C		not specified	Uncertain significance (Jun 29, 2022)
4-42398123-C-A		not specified	Uncertain significance (Feb 22, 2023)
4-42398205-C-T		not specified	Uncertain significance (May 17, 2023)
4-42398210-G-A		not specified	Uncertain significance (Jun 24, 2022)
4-42398247-A-G		not specified	Uncertain significance (Oct 03, 2023)
4-42398258-G-A		not specified	Uncertain significance (Mar 11, 2024)
4-42398300-C-T		not specified	Uncertain significance (Jan 18, 2022)
4-42398303-C-G		not specified	Likely benign (Feb 28, 2023)
4-42401080-G-T		not specified	Uncertain significance (Jan 26, 2022)
4-42401123-C-T		not specified	Uncertain significance (Feb 13, 2023)
4-42401149-C-T		not specified	Uncertain significance (Oct 14, 2023)
4-42401212-C-T		not specified	Uncertain significance (Jun 07, 2024)
4-42401215-C-G		not specified	Uncertain significance (Mar 20, 2023)
4-42401222-G-C		not specified	Uncertain significance (Jan 29, 2024)
4-42401223-C-A		not specified	Uncertain significance (Jan 29, 2024)
4-42401315-C-T		not specified	Uncertain significance (Mar 19, 2024)
4-42401334-C-A		not specified	Uncertain significance (Oct 03, 2022)
4-42401368-G-A		not specified	Uncertain significance (Mar 20, 2023)
4-42401378-A-G		not specified	Uncertain significance (Aug 02, 2021)
4-42401387-C-T		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHISA3	protein_coding	protein_coding	ENST00000319234	2	4649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000364	0.386	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.386	128	141	0.908	0.00000780	1490
Missense in Polyphen		48	48.861	0.98237		520
Synonymous	0.963	53	62.7	0.845	0.00000373	509
Loss of Function	0.213	7	7.64	0.917	3.33e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000433	0.000433
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000642	0.0000615
Middle Eastern	0.000218	0.000217
South Asian	0.000134	0.000131
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in the maturation of presomitic mesoderm cells by individual attenuation of both FGF and WNT signaling. {ECO:0000250}.

Intolerance Scores

• loftool: 0.798
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.408
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0812

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shisa3
• Phenotype: normal phenotype

Gene ontology

• Biological process: multicellular organism development
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: protein binding