SHISA2

shisa family member 2, the group of Shisa family members

Basic information

Region (hg38): 13:26044597-26052016

Previous symbols: [ "C13orf13", "TMEM46" ]

Links

ENSG00000180730 ∙ NCBI:387914 ∙ OMIM:617324 ∙ HGNC:20366 ∙ Uniprot:Q6UWI4 ∙ 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 SHISA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHISA2 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			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	0	0

Variants in SHISA2

This is a list of pathogenic ClinVar variants found in the SHISA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-26046540-C-G		not specified	Uncertain significance (Nov 24, 2024)
13-26046569-A-T		not specified	Uncertain significance (Jan 18, 2025)
13-26046638-C-T		not specified	Uncertain significance (Jun 02, 2024)
13-26046659-C-T		not specified	Uncertain significance (Dec 30, 2024)
13-26046668-G-A		not specified	Uncertain significance (Aug 08, 2022)
13-26046734-T-G		not specified	Uncertain significance (Nov 24, 2024)
13-26046814-C-T		not specified	Uncertain significance (Feb 10, 2023)
13-26046818-C-T		not specified	Uncertain significance (Jan 23, 2024)
13-26046826-T-G		not specified	Uncertain significance (Oct 29, 2024)
13-26046841-G-A		not specified	Uncertain significance (Dec 25, 2024)
13-26046865-C-T		not specified	Uncertain significance (Jan 23, 2024)
13-26046880-C-T		not specified	Uncertain significance (Jul 27, 2021)
13-26046881-G-A		not specified	Uncertain significance (Mar 07, 2025)
13-26046919-A-G		not specified	Uncertain significance (Aug 05, 2024)
13-26046926-G-A		not specified	Uncertain significance (Nov 29, 2023)
13-26046929-T-C		not specified	Uncertain significance (Aug 20, 2024)
13-26046970-C-T		not specified	Uncertain significance (Aug 14, 2024)
13-26046971-G-A		not specified	Uncertain significance (Jul 09, 2024)
13-26046979-C-G		not specified	Uncertain significance (Oct 25, 2023)
13-26046985-C-G		not specified	Uncertain significance (Nov 28, 2024)
13-26047003-G-A		not specified	Uncertain significance (Apr 05, 2023)
13-26047031-C-T		not specified	Uncertain significance (May 01, 2024)
13-26047063-G-A		not specified	Uncertain significance (Oct 26, 2022)
13-26050674-C-G		not specified	Uncertain significance (Feb 06, 2023)
13-26050683-T-C		not specified	Uncertain significance (Jul 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHISA2	protein_coding	protein_coding	ENST00000319420	2	6435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0731	0.878	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0702	163	166	0.985	0.00000952	1882
Missense in Polyphen		75	78.06	0.9608		820
Synonymous	-0.703	76	68.6	1.11	0.00000423	604
Loss of Function	1.67	3	8.13	0.369	4.35e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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}.

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.398
• hipred: Y
• hipred_score: 0.527
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: 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: Shisa2
• 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); growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: multicellular organism development;negative regulation of Wnt signaling pathway;negative regulation of fibroblast growth factor receptor signaling pathway
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane