SHISA4

shisa family member 4, the group of Shisa family members

Basic information

Region (hg38): 1:201888680-201892587

Previous symbols: [ "C1orf40", "TMEM58" ]

Links

ENSG00000198892 ∙ NCBI:149345 ∙ OMIM:617326 ∙ HGNC:27139 ∙ Uniprot:Q96DD7 ∙ 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 SHISA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHISA4 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in SHISA4

This is a list of pathogenic ClinVar variants found in the SHISA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-201889004-G-T		not specified	Uncertain significance (Dec 12, 2023)
1-201889471-T-G		not specified	Uncertain significance (Nov 15, 2024)
1-201889583-C-A		not specified	Uncertain significance (Jan 22, 2024)
1-201889591-C-G		not specified	Uncertain significance (Nov 08, 2024)
1-201890455-C-T		not specified	Uncertain significance (Mar 26, 2024)
1-201890509-G-A		not specified	Uncertain significance (Oct 01, 2024)
1-201890531-T-A		not specified	Uncertain significance (Jul 09, 2024)
1-201890555-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-201891407-A-C		not specified	Uncertain significance (Mar 22, 2023)
1-201891463-A-G		not specified	Uncertain significance (Sep 16, 2021)
1-201891464-A-C		not specified	Uncertain significance (Jan 02, 2024)
1-201891473-C-G		not specified	Uncertain significance (Apr 27, 2022)
1-201891476-C-A		not specified	Uncertain significance (Feb 06, 2023)
1-201891496-A-G		not specified	Uncertain significance (Nov 06, 2024)
1-201891524-A-G		not specified	Uncertain significance (Aug 14, 2024)
1-201891530-C-T		not specified	Uncertain significance (May 20, 2024)
1-201891803-C-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHISA4	protein_coding	protein_coding	ENST00000362011	5	3627

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000927	0.818	125724	0	22	125746	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.943	81	109	0.745	0.00000582	1238
Missense in Polyphen		39	49.173	0.79312		473
Synonymous	0.404	40	43.4	0.922	0.00000235	415
Loss of Function	1.14	6	9.87	0.608	4.23e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.0000880	0.0000879
Middle Eastern	0.000435	0.000435
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.654
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.89

Haploinsufficiency Scores

• pHI: 0.189
• hipred: N
• hipred_score: 0.144
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.115

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shisa4
• Phenotype: normal phenotype

Gene ontology

• Cellular component: integral component of membrane