PPFIA2

PTPRF interacting protein alpha 2, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 12:81257975-81759553

Links

ENSG00000139220 ∙ NCBI:8499 ∙ OMIM:603143 ∙ HGNC:9246 ∙ Uniprot:O75334 ∙ 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 PPFIA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPFIA2 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				3	1	4
missense			43	1	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	43	4	2

Variants in PPFIA2

This is a list of pathogenic ClinVar variants found in the PPFIA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-81263269-G-T		not specified	Uncertain significance (Aug 17, 2022)
12-81263380-T-C		not specified	Uncertain significance (Sep 16, 2021)
12-81266993-T-C		not specified	Uncertain significance (Nov 10, 2022)
12-81267926-T-C		not specified	Uncertain significance (Sep 14, 2023)
12-81268043-C-T			Benign (Jun 27, 2018)
12-81277345-T-G		not specified	Uncertain significance (Dec 13, 2021)
12-81294958-T-G		not specified	Uncertain significance (Jun 03, 2024)
12-81295039-TTAGA-T			Benign (Jun 05, 2018)
12-81325815-G-A			Likely benign (Aug 01, 2022)
12-81325819-T-C		not specified	Uncertain significance (Jan 09, 2024)
12-81325856-T-C		not specified	Uncertain significance (May 05, 2023)
12-81339194-C-T		not specified	Uncertain significance (Aug 15, 2023)
12-81339294-C-G		not specified	Uncertain significance (Jul 09, 2021)
12-81341090-T-C		not specified	Uncertain significance (Feb 07, 2023)
12-81341204-G-T		not specified	Uncertain significance (Apr 26, 2023)
12-81347548-C-T		not specified	Uncertain significance (Jan 10, 2023)
12-81347553-G-A		not specified	Uncertain significance (Dec 18, 2023)
12-81347600-T-C		not specified	Uncertain significance (Mar 08, 2024)
12-81347609-G-A		not specified	Uncertain significance (Mar 04, 2024)
12-81347622-T-C		not specified	Uncertain significance (Mar 19, 2024)
12-81347630-G-A		not specified	Uncertain significance (Apr 29, 2024)
12-81347683-A-G			Benign (Dec 31, 2019)
12-81353170-G-A		not specified	Uncertain significance (Nov 09, 2023)
12-81353186-G-A		not specified	Uncertain significance (Mar 18, 2024)
12-81353224-G-A		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPFIA2	protein_coding	protein_coding	ENST00000549396	30	501288

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.85e-9	124187	0	359	124546	0.00144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.26	406	638	0.637	0.0000334	8109
Missense in Polyphen		91	234.33	0.38834		2948
Synonymous	-0.505	230	220	1.04	0.0000112	2350
Loss of Function	7.51	5	75.4	0.0663	0.00000435	916

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00129	0.00124
Ashkenazi Jewish	0.000202	0.000199
East Asian	0.000352	0.000334
Finnish	0.00920	0.00900
European (Non-Finnish)	0.00119	0.00114
Middle Eastern	0.000352	0.000334
South Asian	0.00	0.00
Other	0.000682	0.000661

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Alters PTPRF cellular localization and induces PTPRF clustering. May regulate the disassembly of focal adhesions. May localize receptor-like tyrosine phosphatases type 2A at specific sites on the plasma membrane, possibly regulating their interaction with the extracellular environment and their association with substrates. {ECO:0000269|PubMed:9624153}.
• Pathway: Neuronal System;Glutamate Neurotransmitter Release Cycle;Dopamine Neurotransmitter Release Cycle;Acetylcholine Neurotransmitter Release Cycle;Neurotransmitter release cycle;Receptor-type tyrosine-protein phosphatases;Transmission across Chemical Synapses;Protein-protein interactions at synapses;Serotonin Neurotransmitter Release Cycle;Norepinephrine Neurotransmitter Release Cycle (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.158
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.77

Haploinsufficiency Scores

• pHI: 0.377
• hipred: Y
• hipred_score: 0.750
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.586

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppfia2
• Phenotype: vision/eye phenotype; 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cell-matrix adhesion;presynapse organization;regulation of synaptic vesicle exocytosis
• Cellular component: cytoplasm;cytosol;cell surface;presynaptic active zone;extracellular exosome;glutamatergic synapse
• Molecular function: protein binding;structural constituent of presynapse