MINDY3

protein-coding

MINDY lysine 48 deubiquitinase 3, the group of MINDY deubiquitinases

Gene summary

The protein encoded by this gene contains a caspase-associated recruitment domain and may function in apoptosis. It has been identified as a tumor suppressor in lung and gastric cancers, and a polymorphism in the gene may be associated with gastric cancer risk. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2015]

Previous symbols:

C10orf97
FAM188A

MANE transcript

NM_024948.4

Inheritance

—

ClinVar variants

U:63B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr10:15,778,170-15,860,507

External References & Databases

Ensembl (ENSG00000148481)

Transcript & Mutation Effects

hg38 • Region Span ~82.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MINDY3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024948.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			61 clinvar	2 clinvar		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	63	2	1	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024948.4	RefSeq	NP_079224.1	15	MANE Select
ENST00000277632.8	Ensembl	ENSP00000277632.3	15	MANE Select
NM_001318330.2	RefSeq	NP_001305259.1	10	Standard
ENST00000378036.5	Ensembl	ENSP00000367275.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

apoptotic process
protein K48-linked deubiquitination

Molecular Function

protein binding
cysteine-type carboxypeptidase activity
thiol-dependent ubiquitinyl hydrolase activity
Lys48-specific deubiquitinase activity

Cellular Component

nucleoplasm
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000277632
Coding exons: 15
Length: 82351
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125748
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.599	203	228	0.888	0.0000110	2895
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): N