PAGE4

PAGE family member 4, the group of PAGE family

Basic information

Region (hg38): X:49793653-49834264

Previous symbols: [ "GAGEC1" ]

Links

ENSG00000101951 ∙ NCBI:9506 ∙ OMIM:300287 ∙ HGNC:4108 ∙ Uniprot:O60829 ∙ 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 PAGE4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAGE4 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	7	0	0

Variants in PAGE4

This is a list of pathogenic ClinVar variants found in the PAGE4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-49830475-A-G		not specified	Uncertain significance (Sep 27, 2024)
X-49830488-T-A		not specified	Uncertain significance (Jul 02, 2024)
X-49830500-C-A		not specified	Uncertain significance (Oct 07, 2024)
X-49830999-C-T			Benign (Jul 23, 2018)
X-49831000-G-A		not specified	Uncertain significance (Aug 11, 2024)
X-49831011-G-C		not specified	Uncertain significance (Jan 04, 2022)
X-49831075-C-T		not specified	Uncertain significance (Jan 03, 2024)
X-49832611-A-C		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAGE4	protein_coding	protein_coding	ENST00000218068	4	4714

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.694	0.290	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0836	35	36.4	0.961	0.00000293	644
Missense in Polyphen		11	7.9777	1.3788		176
Synonymous	0.321	10	11.4	0.879	8.82e-7	187
Loss of Function	1.83	0	3.88	0.00	3.19e-7	71

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0978

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.294
• hipred: N
• hipred_score: 0.203

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function