PPFIA1

PTPRF interacting protein alpha 1, the group of MicroRNA protein coding host genes|Sterile alpha motif domain containing

Basic information

Region (hg38): 11:70270690-70385312

Links

ENSG00000131626 ∙ NCBI:8500 ∙ OMIM:611054 ∙ HGNC:9245 ∙ Uniprot:Q13136 ∙ 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 PPFIA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPFIA1 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				27	6	33
missense			70	3	3	76
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region					1	1
non coding				2	1	3
Total	0	0	70	33	10

Variants in PPFIA1

This is a list of pathogenic ClinVar variants found in the PPFIA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-70272181-C-T		PPFIA1-related disorder	Likely benign (Mar 22, 2019)
11-70272236-C-T		not specified	Uncertain significance (Feb 27, 2023)
11-70272259-G-T		PPFIA1-related disorder	Benign (Mar 21, 2019)
11-70272304-A-G		PPFIA1-related disorder	Likely benign (Feb 21, 2019)
11-70272351-C-T		not specified	Uncertain significance (Jan 20, 2023)
11-70272352-G-C		PPFIA1-related disorder	Likely benign (Sep 03, 2020)
11-70272369-G-T		not specified	Uncertain significance (Aug 15, 2023)
11-70272377-C-T		not specified	Uncertain significance (Jan 31, 2024)
11-70272383-G-A		PPFIA1-related disorder	Benign (Oct 21, 2019)
11-70324965-A-G		not specified	Uncertain significance (Mar 15, 2024)
11-70325568-C-T			Likely benign (Apr 01, 2024)
11-70326267-G-A		not specified	Uncertain significance (Apr 09, 2024)
11-70326308-A-G		not specified	Uncertain significance (Aug 16, 2022)
11-70326314-T-C		not specified	Uncertain significance (Dec 26, 2023)
11-70326346-C-A			Uncertain significance (Oct 08, 2019)
11-70326353-C-T		not specified	Uncertain significance (Jan 06, 2023)
11-70326613-C-T		not specified	Uncertain significance (Jun 28, 2022)
11-70326618-A-C		not specified	Uncertain significance (Jun 24, 2022)
11-70326678-A-G		not specified	Uncertain significance (May 18, 2022)
11-70326708-G-A		not specified	Uncertain significance (Apr 17, 2024)
11-70326755-G-A		PPFIA1-related disorder	Likely benign (Jun 18, 2019)
11-70330273-A-T		not specified	Uncertain significance (Dec 19, 2022)
11-70331967-A-G		PPFIA1-related disorder	Likely benign (May 31, 2022)
11-70331991-G-A		not specified	Uncertain significance (Jun 09, 2022)
11-70332009-A-G		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPFIA1	protein_coding	protein_coding	ENST00000253925	26	113704

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.97e-11	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	618	697	0.887	0.0000413	7899
Missense in Polyphen		172	247.61	0.69463		2771
Synonymous	0.828	249	266	0.935	0.0000167	2301
Loss of Function	7.69	1	70.8	0.0141	0.00000421	760

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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:7796809}.
• 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: 0.112

Intolerance Scores

• loftool: 0.233
• rvis_EVS: -1.68
• rvis_percentile_EVS: 2.69

Haploinsufficiency Scores

• pHI: 0.128
• hipred: Y
• hipred_score: 0.825
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.771

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppfia1

Gene ontology

• Biological process: cell-matrix adhesion;signal transduction;negative regulation of stress fiber assembly;negative regulation of protein localization to plasma membrane
• Cellular component: cytoplasm;cytosol;focal adhesion;presynaptic active zone
• Molecular function: protein binding