MINDY4

MINDY lysine 48 deubiquitinase 4, the group of MINDY deubiquitinases

Basic information

Region (hg38): 7:30771417-30892387

Previous symbols: [ "C7orf67", "FAM188B" ]

Links

ENSG00000106125 ∙ NCBI:84182 ∙ ∙ HGNC:21916 ∙ Uniprot:Q4G0A6 ∙ 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 MINDY4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MINDY4 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				2		2
missense			56	3		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	5	0

Variants in MINDY4

This is a list of pathogenic ClinVar variants found in the MINDY4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-30771555-A-G		not specified	Uncertain significance (Dec 12, 2022)
7-30778440-G-T		not specified	Uncertain significance (Aug 07, 2024)
7-30778468-C-T		not specified	Uncertain significance (Jan 23, 2023)
7-30778474-C-T		not specified	Uncertain significance (Dec 12, 2022)
7-30778483-C-T		not specified	Uncertain significance (Oct 22, 2024)
7-30778504-G-T		not specified	Uncertain significance (Jul 27, 2024)
7-30778512-A-G			Likely benign (Aug 01, 2022)
7-30781983-G-A		not specified	Uncertain significance (Jan 31, 2024)
7-30781983-G-C		not specified	Uncertain significance (May 17, 2023)
7-30782085-C-A		not specified	Uncertain significance (Feb 22, 2023)
7-30782089-C-T		not specified	Uncertain significance (Nov 15, 2024)
7-30782098-A-G		not specified	Uncertain significance (Mar 02, 2023)
7-30782133-A-T		not specified	Uncertain significance (Feb 06, 2024)
7-30782152-A-G		not specified	Uncertain significance (Mar 20, 2024)
7-30785751-A-G		not specified	Uncertain significance (Dec 12, 2023)
7-30785765-G-C		not specified	Uncertain significance (Dec 03, 2024)
7-30785805-C-T		not specified	Uncertain significance (Aug 05, 2024)
7-30785874-T-C		not specified	Likely benign (Dec 15, 2021)
7-30785883-T-G		not specified	Uncertain significance (Mar 07, 2024)
7-30791183-T-C		not specified	Uncertain significance (Jul 20, 2021)
7-30791184-A-G		not specified	Uncertain significance (Aug 10, 2023)
7-30791187-T-C		not specified	Uncertain significance (Dec 08, 2022)
7-30791192-C-T		not specified	Uncertain significance (Oct 06, 2024)
7-30791243-G-A		not specified	Uncertain significance (Dec 01, 2022)
7-30791253-T-C		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MINDY4	protein_coding	protein_coding	ENST00000265299	18	120970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.22e-19	0.0320	124573	0	237	124810	0.000950

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0173	424	425	0.998	0.0000232	4920
Missense in Polyphen		116	115.99	1.0001		1381
Synonymous	-0.372	178	172	1.04	0.00000982	1501
Loss of Function	0.902	32	38.0	0.842	0.00000185	452

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00422	0.00418
Ashkenazi Jewish	0.000697	0.000695
East Asian	0.00162	0.00161
Finnish	0.00	0.00
European (Non-Finnish)	0.000658	0.000644
Middle Eastern	0.00162	0.00161
South Asian	0.000979	0.000948
Other	0.000993	0.000990

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable hydrolase that can remove 'Lys-48'-linked conjugated ubiquitin from proteins. {ECO:0000250|UniProtKB:Q8NBR6}.

Intolerance Scores

• rvis_EVS: 2.25
• rvis_percentile_EVS: 98.21

Haploinsufficiency Scores

• pHI: 0.705
• hipred: N
• hipred_score: 0.144
• ghis: 0.403

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mindy4

Gene ontology

• Biological process: proteolysis
• Molecular function: cysteine-type carboxypeptidase activity;thiol-dependent ubiquitinyl hydrolase activity;Lys48-specific deubiquitinase activity