PAGE1

PAGE family member 1, the group of PAGE family

Basic information

Region (hg38): X:49687446-49695984

Previous symbols: [ "GAGEB1" ]

Links

ENSG00000068985 ∙ NCBI:8712 ∙ OMIM:300288 ∙ HGNC:4107 ∙ Uniprot:O75459 ∙ 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 PAGE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAGE1 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			6		2	8
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	6	0	2

Variants in PAGE1

This is a list of pathogenic ClinVar variants found in the PAGE1 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-49689423-T-C			Benign (Sep 20, 2017)
X-49689435-A-T		not specified	Uncertain significance (Feb 08, 2022)
X-49689453-A-G			Benign (Dec 31, 2019)
X-49689487-G-A		not specified	Uncertain significance (Jan 11, 2023)
X-49691281-C-T		not specified	Uncertain significance (Jun 07, 2024)
X-49691314-C-T		not specified	Uncertain significance (Aug 10, 2021)
X-49691335-G-A		not specified	Uncertain significance (Apr 26, 2023)
X-49691373-C-T			Benign (Aug 09, 2017)
X-49694102-G-C		not specified	Uncertain significance (Mar 22, 2022)
X-49694739-C-T		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAGE1	protein_coding	protein_coding	ENST00000376150	5	8544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.820	0.176	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.129	55	52.4	1.05	0.00000403	941
Missense in Polyphen		13	15.063	0.86302		234
Synonymous	-0.372	21	18.9	1.11	0.00000147	272
Loss of Function	2.21	0	5.67	0.00	4.28e-7	102

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: 0.0960

Intolerance Scores

• loftool: 0.366
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.89

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.158

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

Gene ontology

• Molecular function: protein binding