PPFIA4

PTPRF interacting protein alpha 4, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 1:203026491-203078740

Links

ENSG00000143847 ∙ NCBI:8497 ∙ OMIM:603145 ∙ HGNC:9248 ∙ Uniprot:O75335 ∙ 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 PPFIA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPFIA4 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					2	2
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	30	1	2

Variants in PPFIA4

This is a list of pathogenic ClinVar variants found in the PPFIA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-203043411-A-G			Benign (May 09, 2018)
1-203044000-C-T			Uncertain significance (Mar 01, 2022)
1-203051794-G-A		not specified	Uncertain significance (Oct 07, 2024)
1-203051798-G-A		not specified	Uncertain significance (Jun 17, 2024)
1-203051843-G-A		not specified	Uncertain significance (Jun 16, 2024)
1-203053766-C-G		not specified	Uncertain significance (Feb 21, 2024)
1-203053766-C-T		not specified	Uncertain significance (May 29, 2024)
1-203053819-C-T		not specified	Uncertain significance (Dec 17, 2021)
1-203053831-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-203053871-C-T		not specified	Likely benign (Jan 22, 2024)
1-203053885-C-G		not specified	Uncertain significance (Oct 21, 2021)
1-203053924-C-A		not specified	Uncertain significance (Jan 23, 2023)
1-203055458-C-T		not specified	Uncertain significance (Nov 02, 2021)
1-203055487-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-203055515-T-G		not specified	Uncertain significance (Dec 03, 2021)
1-203055533-G-A		not specified	Uncertain significance (Aug 28, 2024)
1-203055535-A-G		not specified	Uncertain significance (Nov 21, 2023)
1-203055554-C-A		not specified	Uncertain significance (Jul 12, 2022)
1-203055628-C-T		not specified	Uncertain significance (Dec 02, 2022)
1-203055629-G-T		not specified	Uncertain significance (May 24, 2023)
1-203055641-A-G		not specified	Uncertain significance (Apr 08, 2022)
1-203056148-A-G		not specified	Uncertain significance (Sep 22, 2023)
1-203056486-C-G		not specified	Uncertain significance (Nov 28, 2023)
1-203056885-G-A		not specified	Uncertain significance (Apr 06, 2023)
1-203056930-G-A		not specified	Uncertain significance (Nov 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPFIA4	protein_coding	protein_coding	ENST00000272198	17	52243

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000199	1.00	125642	0	25	125667	0.0000995

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	307	421	0.730	0.0000260	4527
Missense in Polyphen		89	127.6	0.69747		1318
Synonymous	1.18	145	164	0.883	0.0000100	1393
Loss of Function	3.22	14	34.3	0.408	0.00000188	382

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000152	0.000150
Middle Eastern	0.000165	0.000163
South Asian	0.0000692	0.0000653
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 (By similarity). {ECO:0000250}.
• 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: 0.114

Intolerance Scores

• loftool: 0.698
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.706
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.632

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppfia4

Gene ontology

• Cellular component: cytosol;cell surface;synapse;presynaptic active zone
• Molecular function: protein binding