PABIR1

PP2A Aalpha (PPP2R1A) and B55A (PPP2R2A) interacting phosphatase regulator 1

Basic information

Region (hg38): 9:68780065-68785566

Previous symbols: [ "C9orf42", "FAM122A" ]

Links

ENSG00000187866 ∙ NCBI:116224 ∙ OMIM:617249 ∙ HGNC:23490 ∙ Uniprot:Q96E09 ∙ 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 PABIR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PABIR1 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	11	0	1

Variants in PABIR1

This is a list of pathogenic ClinVar variants found in the PABIR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-68780097-C-G			Benign (Jun 20, 2018)
9-68780196-A-G		not specified	Uncertain significance (Mar 21, 2023)
9-68780211-C-T		not specified	Uncertain significance (Jan 04, 2024)
9-68780349-G-A		not specified	Uncertain significance (Mar 11, 2024)
9-68780360-C-T		not specified	Uncertain significance (Jul 05, 2023)
9-68780535-G-C		not specified	Uncertain significance (Jul 09, 2021)
9-68780541-A-G		not specified	Uncertain significance (Nov 22, 2023)
9-68780561-T-A		not specified	Uncertain significance (Apr 07, 2022)
9-68780562-C-G		not specified	Uncertain significance (Jun 06, 2023)
9-68780755-T-G		not specified	Uncertain significance (May 14, 2024)
9-68780825-A-G		not specified	Uncertain significance (Aug 11, 2024)
9-68780870-G-T		not specified	Uncertain significance (Feb 09, 2023)
9-68780882-T-C		not specified	Uncertain significance (Mar 07, 2024)
9-68780909-A-C		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PABIR1	protein_coding	protein_coding	ENST00000394264	1	3646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.494	0.488	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	109	161	0.675	0.00000748	1876
Missense in Polyphen		34	63.395	0.53632		777
Synonymous	-0.930	77	67.3	1.14	0.00000345	604
Loss of Function	1.89	1	5.99	0.167	2.67e-7	73

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

• Function: FUNCTION: Acts as an inhibitor of serine/threonine-protein phosphatase 2A (PP2A) activity. Potentiates ubiquitin-mediated proteasomal degradation of serine/threonine-protein phosphatase 2A catalytic subunit alpha (PPP2CA). {ECO:0000269|PubMed:27588481}.

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.573
• hipred: Y
• hipred_score: 0.529
• ghis: 0.543

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.699

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam122a

Gene ontology

• Biological process: positive regulation of cell growth;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of phosphoprotein phosphatase activity
• Molecular function: protein serine/threonine phosphatase inhibitor activity;protein binding