PTPDC1

protein tyrosine phosphatase domain containing 1, the group of CDC14 phosphatases

Basic information

Region (hg38): 9:94030794-94109856

Links

ENSG00000158079 ∙ NCBI:138639 ∙ ∙ HGNC:30184 ∙ Uniprot:A2A3K4 ∙ 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 PTPDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPDC1 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						0
missense			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in PTPDC1

This is a list of pathogenic ClinVar variants found in the PTPDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-94084535-A-G		not specified	Uncertain significance (Dec 26, 2023)
9-94084600-C-T		not specified	Uncertain significance (Nov 27, 2023)
9-94084637-A-G		not specified	Uncertain significance (May 24, 2024)
9-94084655-G-A		not specified	Uncertain significance (Mar 01, 2023)
9-94084666-G-A		not specified	Uncertain significance (Aug 12, 2022)
9-94084676-C-T		not specified	Uncertain significance (Dec 13, 2022)
9-94084680-G-C		not specified	Uncertain significance (Oct 05, 2023)
9-94084691-C-T		not specified	Uncertain significance (Jan 09, 2023)
9-94085301-C-T		not specified	Uncertain significance (Aug 16, 2021)
9-94085353-C-T		not specified	Uncertain significance (May 25, 2022)
9-94085370-C-A		not specified	Uncertain significance (Jun 10, 2024)
9-94088147-A-G		not specified	Uncertain significance (Aug 21, 2023)
9-94095325-T-G		not specified	Uncertain significance (Feb 27, 2023)
9-94095355-G-A		not specified	Uncertain significance (Dec 07, 2021)
9-94097410-A-T		not specified	Uncertain significance (Oct 26, 2022)
9-94097483-C-G		not specified	Uncertain significance (Jan 29, 2024)
9-94097483-C-T		not specified	Uncertain significance (Mar 23, 2023)
9-94097534-G-A		not specified	Uncertain significance (Dec 22, 2023)
9-94097540-G-A		not specified	Uncertain significance (May 09, 2023)
9-94097581-G-A		not specified	Uncertain significance (Feb 10, 2022)
9-94097609-A-G		not specified	Uncertain significance (Feb 13, 2024)
9-94097698-A-G		not specified	Likely benign (Dec 04, 2021)
9-94097716-A-G		not specified	Uncertain significance (Jul 13, 2022)
9-94097839-C-G		not specified	Uncertain significance (Jun 22, 2023)
9-94097930-C-A		not specified	Uncertain significance (Jun 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPDC1	protein_coding	protein_coding	ENST00000288976	9	79063

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000299	1.00	125663	0	85	125748	0.000338

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.817	404	453	0.892	0.0000248	5271
Missense in Polyphen		94	127.51	0.7372		1510
Synonymous	0.865	154	168	0.915	0.00000887	1611
Loss of Function	3.34	14	35.4	0.395	0.00000208	385

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000606	0.000606
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000396	0.000396
Middle Eastern	0.000327	0.000326
South Asian	0.000505	0.000490
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play roles in cilia formation and/or maintenance. {ECO:0000250}.

Intolerance Scores

• loftool: 0.882
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.7

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.332
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.221

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpdc1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: peptidyl-tyrosine dephosphorylation;cilium assembly
• Cellular component: nucleoplasm;cytoplasm
• Molecular function: protein tyrosine phosphatase activity;protein tyrosine/serine/threonine phosphatase activity