PPFIBP2

PPFIA binding protein 2, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 11:7513298-7657127

Links

ENSG00000166387 ∙ NCBI:8495 ∙ OMIM:603142 ∙ HGNC:9250 ∙ Uniprot:Q8ND30 ∙ 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 PPFIBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPFIBP2 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				1		1
missense			69	5	1	75
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	69	6	1

Variants in PPFIBP2

This is a list of pathogenic ClinVar variants found in the PPFIBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-7565562-C-T		not specified	Uncertain significance (Mar 17, 2023)
11-7565567-G-A		not specified	Uncertain significance (Aug 09, 2021)
11-7565610-C-T		not specified	Uncertain significance (Nov 27, 2023)
11-7565612-G-T		not specified	Uncertain significance (Mar 31, 2024)
11-7565628-C-G		not specified	Uncertain significance (Feb 07, 2023)
11-7565639-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-7565670-T-C		not specified	Uncertain significance (Jan 26, 2023)
11-7565684-C-T		not specified	Uncertain significance (Jan 25, 2023)
11-7565700-C-T		not specified	Uncertain significance (Nov 09, 2022)
11-7565720-C-A		not specified	Uncertain significance (May 15, 2023)
11-7565741-A-G		not specified	Uncertain significance (Oct 04, 2022)
11-7565747-G-A		not specified	Uncertain significance (Feb 02, 2024)
11-7565759-G-A		not specified	Uncertain significance (Jul 27, 2022)
11-7593181-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-7593190-G-A		not specified	Uncertain significance (Mar 22, 2024)
11-7593199-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-7597587-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-7597606-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-7597615-A-G		not specified	Uncertain significance (Apr 08, 2022)
11-7610384-G-A		not specified	Uncertain significance (Nov 12, 2021)
11-7620968-A-G		not specified	Uncertain significance (Jun 29, 2023)
11-7620981-T-C		not specified	Uncertain significance (Jun 13, 2024)
11-7625786-G-A		not specified	Uncertain significance (Feb 06, 2023)
11-7625798-G-A		PPFIBP2-related disorder	Likely benign (-)
11-7625810-C-G		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPFIBP2	protein_coding	protein_coding	ENST00000299492	23	143830

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.00e-34	0.0000336	125567	0	181	125748	0.000720

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.12	562	492	1.14	0.0000273	5716
Missense in Polyphen		280	251.22	1.1146		2921
Synonymous	0.212	184	188	0.980	0.0000104	1705
Loss of Function	0.233	52	53.8	0.966	0.00000296	595

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00181	0.00181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000686	0.000677
Middle Eastern	0.000490	0.000489
South Asian	0.00111	0.00111
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate the disassembly of focal adhesions. Did not bind receptor-like tyrosine phosphatases type 2A. {ECO:0000269|PubMed:9624153}.
• Pathway: Ectoderm Differentiation;Neuronal System;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: -0.28
• rvis_percentile_EVS: 33.57

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.350
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.783

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppfibp2

Gene ontology

• Cellular component: extracellular space;cytosol;presynapse
• Molecular function: molecular_function;protein binding;identical protein binding