PAGE2B

PAGE family member 2B, the group of PAGE family

Basic information

Region (hg38): X:55075030-55078909

Links

ENSG00000238269 ∙ NCBI:389860 ∙ ∙ HGNC:31805 ∙ Uniprot:Q5JRK9 ∙ 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 PAGE2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAGE2B 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					1	1
missense			7			7
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	0	1

Variants in PAGE2B

This is a list of pathogenic ClinVar variants found in the PAGE2B 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-55076084-G-A		not specified	Uncertain significance (Jan 20, 2023)
X-55076103-C-A		not specified	Uncertain significance (Jul 02, 2024)
X-55076108-C-G		not specified	Uncertain significance (Feb 23, 2023)
X-55076611-C-T		not specified	Uncertain significance (Mar 18, 2024)
X-55077484-G-T			Benign (Jan 12, 2018)
X-55077501-A-T		not specified	Uncertain significance (Feb 16, 2023)
X-55077503-C-A		not specified	Uncertain significance (Mar 28, 2024)
X-55077521-G-A		not specified	Uncertain significance (Dec 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAGE2B	protein_coding	protein_coding	ENST00000374971	4	3847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00121	0.415	125206	0	2	125208	0.00000799

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.107	39	37.2	1.05	0.00000254	721
Missense in Polyphen		15	13.388	1.1204		273
Synonymous	-0.229	14	13.0	1.08	9.45e-7	204
Loss of Function	-0.211	4	3.57	1.12	2.26e-7	72

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	0.000109	0.0000661
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.646
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.79

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: 0.000187

Gene Damage Prediction

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