PTPN5

protein-coding

protein tyrosine phosphatase non-receptor type 5, the group of Protein tyrosine phosphatases non-receptor type

Gene summary

Enables phosphotyrosine residue binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within protein dephosphorylation. Predicted to be located in membrane and nucleoplasm. Predicted to be active in cell junction; cytosol; and plasma membrane. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006906.2

Inheritance

—

ClinVar variants

U:96B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr11:18,727,928-18,792,721

External References & Databases

Ensembl (ENSG00000110786)

Transcript & Mutation Effects

hg38 • Region Span ~64.8 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 PTPN5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 17

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006906.2. 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			8 clinvar			8
missense			87 clinvar	5 clinvar		92
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	96	5	0	101

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006906.2	RefSeq	NP_008837.1	14	MANE Select
ENST00000358540.7	Ensembl	ENSP00000351342.2	14	MANE Select
NM_001039970.2	RefSeq	NP_001035059.1	14	Standard
NM_001278236.1	RefSeq	NP_001265165.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

MAPK signaling pathway - Homo sapiens (human)
MAPK Signaling Pathway
EGF-EGFR Signaling Pathway

Biological Process

protein dephosphorylation
peptidyl-tyrosine dephosphorylation
cellular response to cytokine stimulus

Molecular Function

phosphotyrosine residue binding
protein tyrosine phosphatase activity
protein binding

Cellular Component

nucleoplasm
endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358540
Coding exons: 14
Length: 64794
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125748
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	294	353	0.833	0.0000220	3658
Missense (PolyPhen)		101	148.45	0.68038		1525
Synonymous	0.218	151	154	0.978	0.0000110	1117
Loss of Function	3.50	11	32.5	0.338	0.00000161	341

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000092	0.000088	rare
South Asian	0.00020	0.00020	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May regulate the activity of several effector molecules involved in synaptic plasticity and neuronal cell survival, including MAPKs, Src family kinases and NMDA receptors. {ECO:0000269|PubMed:21777200}.;

Recessive Scores

pRec: 0.190

Intolerance Scores

LoFtool: 0.498
RVIS EVS: -0.6
RVIS percentile EVS: 18.14

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.761

Gene Damage Prediction

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