MINDY3

MINDY lysine 48 deubiquitinase 3, the group of MINDY deubiquitinases

Basic information

Region (hg38): 10:15778170-15860507

Previous symbols: [ "C10orf97", "FAM188A" ]

Links

ENSG00000148481 ∙ NCBI:80013 ∙ OMIM:611649 ∙ HGNC:23578 ∙ Uniprot:Q9H8M7 ∙ 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 MINDY3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MINDY3 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					2	2
Total	0	0	21	0	3

Variants in MINDY3

This is a list of pathogenic ClinVar variants found in the MINDY3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-15779011-C-T		not specified	Uncertain significance (Nov 22, 2024)
10-15779017-G-A		not specified	Uncertain significance (Nov 09, 2024)
10-15779047-T-C		not specified	Uncertain significance (Jun 01, 2023)
10-15779063-G-A		not specified	Uncertain significance (May 23, 2024)
10-15779079-A-G			Benign (Mar 30, 2018)
10-15782165-T-C		not specified	Uncertain significance (Sep 01, 2021)
10-15786575-A-G		not specified	Uncertain significance (May 13, 2024)
10-15786646-A-G		not specified	Uncertain significance (Oct 26, 2021)
10-15786653-G-A			Benign (Feb 20, 2018)
10-15789272-A-C		not specified	Uncertain significance (Aug 14, 2024)
10-15789302-C-T		not specified	Uncertain significance (Dec 05, 2024)
10-15789328-G-GA			Benign (Jan 24, 2018)
10-15796109-C-G		not specified	Uncertain significance (May 13, 2024)
10-15796156-G-A		not specified	Uncertain significance (Jun 11, 2021)
10-15796157-C-T		not specified	Uncertain significance (Oct 16, 2023)
10-15816849-C-T		not specified	Uncertain significance (Jan 24, 2024)
10-15816857-T-G		not specified	Uncertain significance (Apr 01, 2024)
10-15816864-C-T		not specified	Uncertain significance (Nov 27, 2023)
10-15816887-A-T		not specified	Uncertain significance (Mar 22, 2022)
10-15816894-G-C		not specified	Uncertain significance (Jan 20, 2023)
10-15821713-T-C		not specified	Uncertain significance (Sep 16, 2021)
10-15821734-AAAC-A			Benign (Mar 29, 2018)
10-15833696-T-C		not specified	Uncertain significance (Aug 05, 2024)
10-15834582-G-A		not specified	Uncertain significance (Mar 04, 2024)
10-15834583-C-T		not specified	Uncertain significance (Jun 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MINDY3	protein_coding	protein_coding	ENST00000277632	15	82351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0112	0.989	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.599	203	228	0.888	0.0000110	2895
Missense in Polyphen		47	71.651	0.65596		943
Synonymous	0.419	78	82.8	0.941	0.00000439	814
Loss of Function	3.47	9	29.2	0.308	0.00000131	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000122
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000171	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolase that can remove 'Lys-48'-linked conjugated ubiquitin from proteins. {ECO:0000269|PubMed:27292798}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.91
• rvis_percentile_EVS: 9.9

Haploinsufficiency Scores

• pHI: 0.429
• hipred: Y
• hipred_score: 0.543
• ghis: 0.639

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mindy3

Gene ontology

• Biological process: apoptotic process;protein K48-linked deubiquitination
• Cellular component: nucleoplasm;nuclear membrane
• Molecular function: protein binding;cysteine-type carboxypeptidase activity;thiol-dependent ubiquitinyl hydrolase activity;Lys48-specific deubiquitinase activity