PAGE2

PAGE family member 2, the group of PAGE family

Basic information

Region (hg38): X:55089018-55092842

Previous symbols: [ "GAGEC2" ]

Links

ENSG00000234068 ∙ NCBI:203569 ∙ OMIM:300738 ∙ HGNC:31804 ∙ Uniprot:Q7Z2X7 ∙ 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 PAGE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAGE2 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				2		2
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	3	0

Variants in PAGE2

This is a list of pathogenic ClinVar variants found in the PAGE2 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-55090089-G-A			Likely benign (May 01, 2022)
X-55090103-T-C		not specified	Uncertain significance (Feb 12, 2024)
X-55090526-C-T		not specified	Uncertain significance (Aug 12, 2021)
X-55090554-A-G		not specified	Uncertain significance (Dec 07, 2021)
X-55090566-C-T		not specified	Uncertain significance (Jul 02, 2024)
X-55090580-A-T		not specified	Uncertain significance (Jul 14, 2021)
X-55090582-T-C			Likely benign (Apr 01, 2022)
X-55090604-T-G		not specified	Likely benign (Feb 16, 2023)
X-55091342-G-A		not specified	Uncertain significance (Oct 30, 2023)
X-55091400-C-T		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAGE2	protein_coding	protein_coding	ENST00000374968	4	3835

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0572	0.725	125060	0	2	125062	0.00000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.442	44	36.5	1.21	0.00000243	720
Missense in Polyphen		21	13.553	1.5494		281
Synonymous	-0.390	14	12.3	1.14	8.51e-7	207
Loss of Function	0.772	2	3.58	0.559	2.26e-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)	0.0000252	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0321

Intolerance Scores

• loftool: 0.711
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.45

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0169

Gene Damage Prediction

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

Gene ontology

• Molecular function: protein binding