MINDY1

MINDY lysine 48 deubiquitinase 1, the group of MINDY deubiquitinases

Basic information

Region (hg38): 1:150996548-151008376

Previous symbols: [ "FAM63A" ]

Links

ENSG00000143409 ∙ NCBI:55793 ∙ OMIM:618407 ∙ HGNC:25648 ∙ Uniprot:Q8N5J2 ∙ 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 MINDY1 gene.

• Inborn genetic diseases (8 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MINDY1 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	7	2	0

Variants in MINDY1

This is a list of pathogenic ClinVar variants found in the MINDY1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-150997331-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-150997337-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-150997338-G-A			Likely benign (Feb 01, 2023)
1-150997360-C-T		not specified	Uncertain significance (Sep 06, 2022)
1-150997643-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-150997647-G-A		not specified	Uncertain significance (Aug 31, 2022)
1-150997652-C-T		not specified	Uncertain significance (Jan 10, 2022)
1-150997776-A-G		not specified	Uncertain significance (Jan 10, 2022)
1-150998174-C-T		not specified	Uncertain significance (Mar 27, 2023)
1-150998254-A-G		not specified	Uncertain significance (Aug 01, 2022)
1-150999371-T-C		not specified	Uncertain significance (Jan 25, 2023)
1-150999478-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-150999497-G-T		not specified	Uncertain significance (Jan 26, 2022)
1-150999871-C-T		not specified	Uncertain significance (Nov 16, 2022)
1-150999958-C-T		not specified	Uncertain significance (Aug 31, 2022)
1-151000485-A-G		not specified	Uncertain significance (Dec 28, 2023)
1-151001770-G-C		not specified	Uncertain significance (Jul 13, 2021)
1-151002208-C-A		not specified	Uncertain significance (May 11, 2022)
1-151002215-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-151002313-T-G		not specified	Uncertain significance (Feb 10, 2022)
1-151002352-T-C		not specified	Uncertain significance (Jul 14, 2021)
1-151002385-G-A		not specified	Likely benign (Jan 17, 2023)
1-151002386-G-C		not specified	Uncertain significance (Aug 22, 2023)
1-151002406-G-A		not specified	Uncertain significance (Sep 14, 2023)
1-151002517-T-C		not specified	Uncertain significance (Nov 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MINDY1	protein_coding	protein_coding	ENST00000361738	10	11827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.55e-16	0.0234	125650	0	97	125747	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	233	291	0.800	0.0000160	3351
Missense in Polyphen		85	116.08	0.73223		1435
Synonymous	-1.26	139	121	1.15	0.00000691	1062
Loss of Function	0.419	25	27.4	0.913	0.00000153	270

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00124
Ashkenazi Jewish	0.00	0.00
East Asian	0.000443	0.000435
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.000349	0.000343
Middle Eastern	0.000443	0.000435
South Asian	0.000235	0.000229
Other	0.000818	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolase that can specifically remove 'Lys-48'-linked conjugated ubiquitin from proteins. Has exodeubiquitinase activity and has a preference for long polyubiquitin chains. May play a regulatory role at the level of protein turnover. {ECO:0000269|PubMed:27292798, ECO:0000269|PubMed:28082312}.

Recessive Scores

• pRec: 0.0637

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.69

Haploinsufficiency Scores

• pHI: 0.0657
• hipred: N
• hipred_score: 0.196
• ghis: 0.414

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mindy1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; limbs/digits/tail phenotype; vision/eye phenotype; immune system phenotype

Gene ontology

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