DUSP29

dual specificity phosphatase 29, the group of Atypical dual specificity phosphatases

Basic information

Region (hg38): 10:75037471-75073642

Previous symbols: [ "DUPD1" ]

Links

ENSG00000188716 ∙ NCBI:338599 ∙ OMIM:618574 ∙ HGNC:23481 ∙ Uniprot:Q68J44 ∙ 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 DUSP29 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUSP29 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in DUSP29

This is a list of pathogenic ClinVar variants found in the DUSP29 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-75037870-T-C		not specified	Uncertain significance (Oct 06, 2023)
10-75037885-C-T		not specified	Uncertain significance (Feb 16, 2023)
10-75037945-G-A		not specified	Uncertain significance (Apr 23, 2024)
10-75037999-T-A		not specified	Uncertain significance (Aug 03, 2022)
10-75038002-T-C		not specified	Likely benign (Jan 18, 2023)
10-75038047-C-T		not specified	Uncertain significance (Jul 20, 2021)
10-75038050-C-A		not specified	Uncertain significance (Jan 10, 2023)
10-75038072-T-C		not specified	Uncertain significance (Jun 01, 2022)
10-75043838-G-C		not specified	Uncertain significance (May 23, 2024)
10-75043853-C-G		not specified	Uncertain significance (Mar 11, 2022)
10-75043865-G-A		not specified	Uncertain significance (Jun 24, 2022)
10-75043872-G-C		not specified	Likely benign (Jan 07, 2022)
10-75043923-C-T		not specified	Uncertain significance (Jun 06, 2023)
10-75043925-G-A		not specified	Uncertain significance (Mar 24, 2023)
10-75043968-C-T		not specified	Uncertain significance (Dec 05, 2022)
10-75058353-G-C		not specified	Uncertain significance (Dec 20, 2023)
10-75058353-G-T		not specified	Uncertain significance (Apr 18, 2023)
10-75058388-G-A		not specified	Uncertain significance (Aug 04, 2023)
10-75058402-G-C		not specified	Uncertain significance (Jun 07, 2023)
10-75058417-T-C		not specified	Uncertain significance (May 14, 2024)
10-75058489-C-T		not specified	Uncertain significance (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUSP29	protein_coding	protein_coding	ENST00000338487	3	20679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.48e-7	0.0889	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.594	133	154	0.865	0.0000108	1439
Missense in Polyphen		48	62.939	0.76264		572
Synonymous	0.917	61	70.8	0.861	0.00000549	438
Loss of Function	-0.686	9	7.04	1.28	2.99e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000653	0.000653
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dual specificity phosphatase able to dephosphorylate phosphotyrosine, phosphoserine and phosphothreonine residues, with a preference for phosphotyrosine as a substrate. {ECO:0000269|PubMed:17498703}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.465
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.301
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: Dupd1

Gene ontology

• Biological process: protein dephosphorylation;peptidyl-tyrosine dephosphorylation
• Cellular component: cytoplasm;protein-containing complex
• Molecular function: protein tyrosine phosphatase activity;protein tyrosine/serine/threonine phosphatase activity;protein homodimerization activity