PAGR1

PAXIP1 associated glutamate rich protein 1

Basic information

Region (hg38): 16:29816152-29822489

Previous symbols: [ "C16orf53" ]

Links

ENSG00000280789 ∙ NCBI:79447 ∙ OMIM:612033 ∙ HGNC:28707 ∙ Uniprot:Q9BTK6 ∙ 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 PAGR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAGR1 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		1	12	3		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	1	12	3	1

Variants in PAGR1

This is a list of pathogenic ClinVar variants found in the PAGR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-29816536-C-T		not specified	Likely benign (Jul 25, 2023)
16-29816554-C-T		not specified	Likely benign (Jul 06, 2021)
16-29816557-C-T		not specified	Uncertain significance (Jun 09, 2022)
16-29816562-A-T		not specified	Uncertain significance (Jun 10, 2022)
16-29816580-T-C		not specified	Uncertain significance (May 13, 2024)
16-29816679-G-A		not specified	Uncertain significance (May 26, 2022)
16-29816697-G-A		not specified	Uncertain significance (Sep 25, 2023)
16-29816709-T-C		not specified	Uncertain significance (Oct 20, 2024)
16-29816710-C-T		not specified	Uncertain significance (Aug 19, 2023)
16-29816731-G-C		not specified	Uncertain significance (Nov 08, 2022)
16-29816742-A-C		not specified	Uncertain significance (Mar 21, 2023)
16-29816763-G-C		not specified	Uncertain significance (Dec 07, 2021)
16-29816770-A-G		not specified	Likely benign (Dec 27, 2023)
16-29816799-A-G		lethal neurodevelopmental disorder • Neurodevelopmental disorder	Conflicting classifications of pathogenicity (Nov 26, 2024)
16-29816811-G-T		not specified	Uncertain significance (Sep 26, 2024)
16-29816844-C-A		not specified	Uncertain significance (May 28, 2024)
16-29816899-T-C		not specified	Uncertain significance (Feb 28, 2023)
16-29816913-G-A		not specified	Uncertain significance (Aug 15, 2023)
16-29816929-G-A		not specified	Uncertain significance (Jun 03, 2022)
16-29816941-C-G		not specified	Uncertain significance (Dec 10, 2024)
16-29817257-C-G		not specified	Uncertain significance (Dec 17, 2023)
16-29819546-C-T			Benign (May 16, 2018)
16-29819695-G-T		not specified	Uncertain significance (Oct 12, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Its association with the histone methyltransferase MLL2/MLL3 complex is suggesting a role in epigenetic transcriptional activation. However, in association with PAXIP1/PTIP is proposed to function at least in part independently of the MLL2/MLL3 complex. Proposed to be recruited by PAXIP1 to sites of DNA damage where the PAGR1:PAXIP1 complex is required for cell survival in response to DNA damage independently of the MLL2/MLL3 complex (PubMed:19124460). However, its function in DNA damage has been questioned (By similarity). During immunoglobulin class switching in activated B-cells is involved in transcription regulation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus independently of the MLL2/MLL3 complex (By similarity). Involved in both estrogen receptor-regulated gene transcription and estrogen-stimulated G1/S cell-cycle transition (PubMed:19039327). Acts as transcriptional cofactor for nuclear hormone receptors. Inhibits the induction properties of several steroid receptors such as NR3C1, AR and PPARG; the mechanism of inhibition appears to be gene-dependent (PubMed:23161582). {ECO:0000250|UniProtKB:Q99L02, ECO:0000269|PubMed:19039327, ECO:0000269|PubMed:19124460, ECO:0000269|PubMed:23161582, ECO:0000305}.

Recessive Scores

• pRec: 0.243

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.210

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pagr1a
• Phenotype: cellular phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype

Zebrafish Information Network

• Gene name: pagr1
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: DNA repair;DNA recombination;positive regulation of intracellular estrogen receptor signaling pathway;positive regulation of transcription by RNA polymerase II;histone H3-K4 methylation;positive regulation of cell cycle G1/S phase transition
• Cellular component: nucleus;histone methyltransferase complex;MLL3/4 complex
• Molecular function: protein binding;estrogen receptor binding