SHISA5

protein-coding

shisa family member 5, the group of Shisa family members

Gene summary

This gene encodes a member of the shisa family. The encoded protein is localized to the endoplasmic reticulum, and together with p53 induces apoptosis in a caspase-dependent manner. Alternative splicing results in multiple transcript variants. Related pseudogenes of this gene are found on chromosome X. [provided by RefSeq, Apr 2016]

MANE transcript

NM_016479.6

Inheritance

—

ClinVar variants

U:28B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr3:48,467,798-48,504,826

External References & Databases

Ensembl (ENSG00000164054)

Transcript & Mutation Effects

hg38 • Region Span ~37.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SHISA5 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016479.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			21 clinvar	1 clinvar		22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	28	1	0	29

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016479.6	RefSeq	NP_057563.3	6	MANE Select
ENST00000296444.7	Ensembl	ENSP00000296444.2	6	MANE Select
NM_001272065.3	RefSeq	NP_001258994.1	6	Standard
NM_001272066.2	RefSeq	NP_001258995.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

protein binding

Cellular Component

endoplasmic reticulum
endoplasmic reticulum lumen
endoplasmic reticulum membrane
integral component of membrane
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296444
Coding exons: 6
Length: 33063
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125742
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.285	141	151	0.935	0.00000930	1509
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000089	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00026	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0961

Intolerance Scores

LoFtool: 0.824
RVIS EVS: -0.2
RVIS percentile EVS: 38.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.167

Gene Damage Prediction

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