PPFIA4

protein-coding

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

Gene summary

PPFIA4, or liprin-alpha-4, belongs to the liprin-alpha gene family. See liprin-alpha-1 (LIP1, or PPFIA1; MIM 611054) for background on liprins.[supplied by OMIM, Mar 2008]

MANE transcript

NM_001304331.2

Inheritance

—

ClinVar variants

U:75B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr1:203,026,491-203,078,740

External References & Databases

Ensembl (ENSG00000143847)

Transcript & Mutation Effects

hg38 • Region Span ~52.2 kb

Loading mutation effect viewer...

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 PPFIA4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001304331.2. 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				1 clinvar	2 clinvar	3
missense			73 clinvar	1 clinvar		74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	75	2	2	79

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001304331.2	RefSeq	NP_001291260.1	29	MANE Select
ENST00000295706.9	Ensembl	ENSP00000295706.5	29	MANE Select
NM_001304332.2	RefSeq	NP_001291261.1	28	Standard
NM_001393950.1	RefSeq	NP_001380879.1	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neuronal System
Glutamate Neurotransmitter Release Cycle
Dopamine Neurotransmitter Release Cycle
Acetylcholine Neurotransmitter Release Cycle
Neurotransmitter release cycle

Molecular Function

protein binding

Cellular Component

cytosol
cell surface
synapse
presynaptic active zone

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272198
Coding exons: 17
Length: 52243
Individuals with no LoFs: 125642
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125667
p: 0.0000995

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.97	307	421	0.730	0.0000260	4527
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000071	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.000069	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.114

Intolerance Scores

LoFtool: 0.698
RVIS EVS: -0.44
RVIS percentile EVS: 24.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.632

Gene Damage Prediction

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