PPFIBP2

protein-coding

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

Gene summary

This gene encodes a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. The encoded protein is a beta liprin and plays a role in axon guidance and neuronal synapse development by recruiting LAR protein-tyrosine phosphatases to the plasma membrane. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

MANE transcript

NM_003621.5

Inheritance

—

ClinVar variants

U:172B:10

Top phenotype

PPFIBP2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr11:7,513,298-7,657,127

External References & Databases

Ensembl (ENSG00000166387)

Transcript & Mutation Effects

hg38 • Region Span ~143.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPFIBP2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 158

not providedTotal: 5

PPFIBP2-related disorderTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003621.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar		5
missense			157 clinvar	7 clinvar	1 clinvar	165
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	172	9	1	182

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 62 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003621.5	RefSeq	NP_003612.3	23	MANE Select
ENST00000299492.9	Ensembl	ENSP00000299492.4	23	MANE Select
NM_001256568.2	RefSeq	NP_001243497.2	21	Standard
NM_001256569.2	RefSeq	NP_001243498.2	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation
Neuronal System
Receptor-type tyrosine-protein phosphatases
Protein-protein interactions at synapses

Molecular Function

molecular_function
protein binding
identical protein binding

Cellular Component

extracellular space
cytosol
presynapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000299492
Coding exons: 23
Length: 143830
Individuals with no LoFs: 125567
Homozygous LoFs: 0
Heterozygous LoFs: 181
Defined: 125748
p: 0.000720

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.12	562	492	1.14	0.0000273	5716
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00069	0.00068	rare
South Asian	0.0011	0.0011	notable
Other	0.0011	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May regulate the disassembly of focal adhesions. Did not bind receptor-like tyrosine phosphatases type 2A. {ECO:0000269|PubMed:9624153}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

RVIS EVS: -0.28
RVIS percentile EVS: 33.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.783

Gene Damage Prediction

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