MINDY2

MINDY lysine 48 deubiquitinase 2, the group of MINDY deubiquitinases

Basic information

Region (hg38): 15:58771192-58861900

Previous symbols: [ "FAM63B" ]

Links

ENSG00000128923 ∙ NCBI:54629 ∙ OMIM:618408 ∙ HGNC:26954 ∙ Uniprot:Q8NBR6 ∙ 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 MINDY2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MINDY2 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			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in MINDY2

This is a list of pathogenic ClinVar variants found in the MINDY2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-58771495-A-T		not specified	Uncertain significance (Oct 12, 2021)
15-58771504-G-C		not specified	Uncertain significance (Mar 04, 2024)
15-58771522-G-A		not specified	Uncertain significance (Apr 18, 2023)
15-58771525-T-A		not specified	Uncertain significance (Dec 03, 2021)
15-58771610-C-G		not specified	Uncertain significance (Mar 20, 2023)
15-58771627-C-T		not specified	Uncertain significance (Mar 01, 2024)
15-58771645-G-T		not specified	Uncertain significance (Jan 23, 2024)
15-58771703-G-A		not specified	Uncertain significance (Apr 18, 2023)
15-58771706-G-A		not specified	Uncertain significance (Sep 16, 2021)
15-58771724-C-T		not specified	Uncertain significance (Aug 12, 2021)
15-58771736-C-T		not specified	Uncertain significance (Jan 23, 2024)
15-58771751-T-C		not specified	Likely benign (Dec 20, 2023)
15-58771835-G-T		not specified	Uncertain significance (Mar 28, 2024)
15-58771870-A-G		not specified	Uncertain significance (May 23, 2023)
15-58771946-C-A		not specified	Uncertain significance (Jan 10, 2022)
15-58771958-G-T		not specified	Uncertain significance (Sep 16, 2021)
15-58771993-A-G		not specified	Uncertain significance (Dec 13, 2023)
15-58772050-A-C		not specified	Uncertain significance (Mar 07, 2024)
15-58772055-G-C		not specified	Uncertain significance (Dec 01, 2022)
15-58772062-G-C		not specified	Uncertain significance (Aug 09, 2021)
15-58772071-A-G		not specified	Likely benign (Jul 08, 2022)
15-58772093-C-T		not specified	Uncertain significance (Oct 12, 2021)
15-58772128-A-G		not specified	Uncertain significance (May 01, 2024)
15-58787930-A-G		not specified	Uncertain significance (Aug 20, 2023)
15-58802360-C-T		not specified	Uncertain significance (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MINDY2	protein_coding	protein_coding	ENST00000559228	9	90709

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000176	0.999	124765	0	29	124794	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.559	361	332	1.09	0.0000161	4041
Missense in Polyphen		104	127.68	0.81451		1700
Synonymous	-2.34	164	130	1.26	0.00000648	1202
Loss of Function	2.83	13	29.6	0.439	0.00000150	339

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000331
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.000104	0.0000971
Middle Eastern	0.0000556	0.0000556
South Asian	0.000175	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolase that can remove 'Lys-48'-linked conjugated ubiquitin from proteins (PubMed:27292798). Binds to polyubiquitin chains of different linkage types, including 'Lys-6', 'Lys-11', 'Lys-29', 'Lys-33', 'Lys-48' and 'Lys-63' (PubMed:28082312). May play a regulatory role at the level of protein turnover (PubMed:27292798). {ECO:0000269|PubMed:27292798, ECO:0000269|PubMed:28082312}.

Intolerance Scores

• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.426
• ghis: 0.574

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mindy2

Gene ontology

• Biological process: biological_process;protein K48-linked deubiquitination
• Cellular component: nucleoplasm;cytosol
• Molecular function: thiol-dependent ubiquitin-specific protease activity;cysteine-type carboxypeptidase activity;K48-linked polyubiquitin modification-dependent protein binding;K63-linked polyubiquitin modification-dependent protein binding;K11-linked polyubiquitin modification-dependent protein binding;K6-linked polyubiquitin modification-dependent protein binding;Lys48-specific deubiquitinase activity