PTPN4

protein tyrosine phosphatase non-receptor type 4, the group of FERM domain containing|Protein tyrosine phosphatases non-receptor type|PDZ domain containing

Basic information

Region (hg38): 2:119759922-119984899

Links

ENSG00000088179 ∙ NCBI:5775 ∙ OMIM:176878 ∙ HGNC:9656 ∙ Uniprot:P29074 ∙ 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 PTPN4 gene.

• Neurodevelopmental disorder (1 variants)
• PTPN4-related disorder (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN4 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			66	5	1	72
nonsense	2	1	1			4
start loss						0
frameshift		1	2			3
inframe indel						0
splice donor/acceptor (+/-2bp)		3	2			5
splice region			1			1
non coding					1	1
Total	2	5	71	6	2

Variants in PTPN4

This is a list of pathogenic ClinVar variants found in the PTPN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-119809896-G-A		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
2-119809906-C-T		Inborn genetic diseases	Uncertain significance (Dec 16, 2024)
2-119809918-G-A		Inborn genetic diseases	Uncertain significance (Aug 10, 2024)
2-119809936-A-C		Inborn genetic diseases	Uncertain significance (Nov 26, 2024)
2-119809948-A-C		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)
2-119809968-A-G		Inborn genetic diseases	Uncertain significance (Jan 23, 2025)
2-119809969-C-G		Inborn genetic diseases	Uncertain significance (Nov 11, 2024)
2-119809978-C-A		Inborn genetic diseases	Uncertain significance (Mar 10, 2025)
2-119809990-A-G		Inborn genetic diseases	Uncertain significance (Aug 16, 2022)
2-119809993-T-C			Likely pathogenic (Nov 14, 2022)
2-119862538-A-T		Inborn genetic diseases	Uncertain significance (Oct 27, 2022)
2-119862545-CA-C		Neurodevelopmental disorder	Likely pathogenic (Jul 16, 2023)
2-119862569-G-A		Inborn genetic diseases	Uncertain significance (Nov 02, 2023)
2-119862588-T-G			Uncertain significance (Nov 04, 2020)
2-119862599-G-A		PTPN4-related disorder	Uncertain significance (Sep 05, 2024)
2-119862632-A-G		Inborn genetic diseases	Uncertain significance (Sep 04, 2024)
2-119862644-G-T			Likely pathogenic (Nov 29, 2022)
2-119877328-G-T		not specified	Uncertain significance (Mar 06, 2024)
2-119877347-A-G		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
2-119877486-C-A		Inborn genetic diseases	Uncertain significance (Jun 30, 2022)
2-119881807-TAAAC-T			Uncertain significance (Nov 04, 2020)
2-119881816-C-A		PTPN4-related disorder	Uncertain significance (Feb 02, 2023)
2-119882119-G-A		Inborn genetic diseases	Uncertain significance (Jul 08, 2024)
2-119882508-C-A		PTPN4-related disorder	Likely benign (Apr 28, 2022)
2-119882574-C-T		PTPN4-related aberrant neurodevelopment and growth	Likely pathogenic (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN4	protein_coding	protein_coding	ENST00000263708	26	224188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00337	125724	0	20	125744	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.65	314	477	0.659	0.0000242	6058
Missense in Polyphen		95	204.25	0.46512		2531
Synonymous	2.55	122	164	0.746	0.00000798	1697
Loss of Function	6.04	10	60.9	0.164	0.00000362	705

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000277	0.000270
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000982	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act at junctions between the membrane and the cytoskeleton.
• Pathway: Toll-Like Receptors Cascades;Innate Immune System;Immune System;Toll Like Receptor 4 (TLR4) Cascade (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.343
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.15

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.662
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.957

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpn4
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein dephosphorylation;peptidyl-tyrosine dephosphorylation;cellular response to cytokine stimulus
• Cellular component: nucleoplasm;cytoplasm;cytosol;cytoskeleton;cytoplasmic side of plasma membrane
• Molecular function: non-membrane spanning protein tyrosine phosphatase activity;protein binding;cytoskeletal protein binding