DUSP29

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

Basic information

Region (hg38): 10:75037472-75073642

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.

• not_specified (47 variants)

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. These statistics are base on transcript: NM_001003892.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			42	5		47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	5	0

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