MINDY4B

Summary

MINDY4B (MINDY family member 4B, HGNC:35475) is a protein-coding gene on chromosome 3q25.1, encoding Inactive ubiquitin carboxyl-terminal hydrolase MINDY-4B (A8MYZ0).

Predicted to enable K48-linked deubiquitinase activity. Predicted to be involved in protein K48-linked deubiquitination.

Source: NCBI Gene 646951 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001351281

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:35475
Approved symbol	MINDY4B
Name	MINDY family member 4B
Location	3q25.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000214237
Ensembl biotype	protein_coding
Entrez	646951

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000465419, ENST00000474598

RefSeq mRNA: 1 — MANE Select: NM_001351281 NM_001351281

CCDS: CCDS93407

Canonical transcript exons

ENST00000465419 — 12 exons

Exon	Start	End
ENSE00001861368	150890938	150891103
ENSE00002356232	150882897	150883058
ENSE00002364651	150873187	150873367
ENSE00003520103	150870376	150871187
ENSE00003583678	150890320	150890385
ENSE00003644303	150885368	150885438
ENSE00003676935	150883700	150883772
ENSE00003803990	150894186	150894305
ENSE00003804612	150903249	150903416
ENSE00003804870	150905062	150905089
ENSE00003804943	150905327	150905439
ENSE00003805440	150893324	150893415

Expression profiles

Bgee: expression breadth broad, 67 present calls, max score 98.38.

Top tissues by expression

106 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	98.38	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	95.38	gold quality
nucleus accumbens	UBERON:0001882	68.32	gold quality
caudate nucleus	UBERON:0001873	66.81	gold quality
putamen	UBERON:0001874	62.23	gold quality
right adrenal gland cortex	UBERON:0035827	59.28	gold quality
right adrenal gland	UBERON:0001233	56.96	gold quality
adrenal tissue	UBERON:0018303	56.37	gold quality
blood	UBERON:0000178	52.33	gold quality
Brodmann (1909) area 9	UBERON:0013540	47.17	gold quality
apex of heart	UBERON:0002098	47.10	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	46.33	gold quality
adrenal gland	UBERON:0002369	46.22	gold quality
left adrenal gland	UBERON:0001234	45.30	gold quality
superior frontal gyrus	UBERON:0002661	45.20	gold quality
prefrontal cortex	UBERON:0000451	44.19	gold quality
left adrenal gland cortex	UBERON:0035825	44.09	gold quality
frontal cortex	UBERON:0001870	43.26	gold quality
right frontal lobe	UBERON:0002810	41.98	gold quality
colonic epithelium	UBERON:0000397	41.52	gold quality
right uterine tube	UBERON:0001302	40.77	silver quality
ventricular zone	UBERON:0003053	40.56	silver quality
brain	UBERON:0000955	40.28	gold quality
cerebral cortex	UBERON:0000956	39.32	gold quality
hindlimb stylopod muscle	UBERON:0004252	38.88	gold quality
pituitary gland	UBERON:0000007	38.47	gold quality
sural nerve	UBERON:0015488	38.07	gold quality
ganglionic eminence	UBERON:0004023	37.19	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.62

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	mindy4b	ENSDARG00000112337
mus_musculus	Mindy4b-ps	ENSMUSG00000101860
rattus_norvegicus	Mindy4b	ENSRNOG00000043502

Paralogs (2): MINDY4 (ENSG00000106125), MINDY3 (ENSG00000148481)

Protein

Protein identifiers

Inactive ubiquitin carboxyl-terminal hydrolase MINDY-4B — A8MYZ0 (reviewed: A8MYZ0)

Alternative names: Protein FAM188B2

All UniProt accessions (1): A8MYZ0

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the MINDY deubiquitinase family. FAM188 subfamily.

RefSeq proteins (1): NP_001338210* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025257	MINDY-3/4_CD	Domain
IPR039785	MINY3/4	Family

Pfam: PF13898

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MYZ0-F1	83.35	0.63

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): GOBP_PROTEIN_MODIFICATION_BY_SMALL_PROTEIN_REMOVAL, GOMF_CYSTEINE_TYPE_PEPTIDASE_ACTIVITY, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_K48_LINKED_DEUBIQUITINATION, GOMF_PEPTIDASE_ACTIVITY, GOMF_UBIQUITIN_LIKE_PROTEIN_PEPTIDASE_ACTIVITY, chr3q25, GOMF_K48_LINKED_DEUBIQUITINASE_ACTIVITY, ZNF274_TARGET_GENES, BPTF_TARGET_GENES, GOBP_PROTEIN_MODIFICATION_PROCESS, GOMF_DEUBIQUITINASE_ACTIVITY

GO Biological Process (1): protein K48-linked deubiquitination (GO:0071108)

GO Molecular Function (2): cysteine-type deubiquitinase activity (GO:0004843), K48-linked deubiquitinase activity (GO:1990380)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
deubiquitinase activity	2
protein deubiquitination	1
cysteine-type peptidase activity	1

Protein interactions and networks

STRING

168 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MINDY4B	OR1E2	P47887	507
MINDY4B	ZNF562	Q6V9R5	475
MINDY4B	OR1E1	P30953	445
MINDY4B	ZBTB8B	Q8NAP8	432
MINDY4B	C8orf34	Q49A92	380
MINDY4B	PTPDC1	A2A3K4	371
MINDY4B	ZNF101	Q8IZC7	370
MINDY4B	QSER1	Q2KHR3	367
MINDY4B	CCDC47	Q96A33	355
MINDY4B	PGBD1	Q96JS3	348
MINDY4B	EID2	Q8N6I1	348
MINDY4B	HSD17B2	P37059	333
MINDY4B	RBM24	Q9BX46	327
MINDY4B	SLC35B1	P78383	325
MINDY4B	SFSWAP	Q12872	323
MINDY4B	RAB44	Q7Z6P3	323

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0AUR5, A0JNG7, A2VE39, A5PKL6, A8MYZ0, B0BM95, B0V3H4, B5DG51, D2HRF1, O02697, P48736, P60670, Q0IIH8, Q4KLT3, Q4R4D7, Q4R528, Q4R6Y8, Q4R760, Q4V8W7, Q5R981, Q5RBW9, Q5RL51, Q5U2Z5, Q5XH30, Q68EP9, Q6NX27, Q7ZYP6, Q803A6, Q803R5, Q80V94, Q811C2, Q8CD92, Q8CDM8, Q8K4M9, Q8N1G2, Q8NEC7, Q8R3N6, Q8TAT6, Q8VDY4, Q91WR3

Diamond homologs: A1A4L4, A8MYZ0, Q0VA42, Q3UQI9, Q4G0A6, Q5RF72, Q6NX27, Q9CV28, Q0IIH8, A0AUR5, D2DGW3, Q1A7B1, Q4R528, Q9H8M7, Q9VWN5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

0 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1534 predictions. Top by Δscore:

Variant	Effect	Δscore
3:150885439:C:CC	acceptor_gain	1.0000
3:150885444:C:CT	acceptor_gain	1.0000
3:150890313:CACT:C	donor_loss	1.0000
3:150890314:ACTT:A	donor_loss	1.0000
3:150890315:CTTA:C	donor_loss	1.0000
3:150890316:TTAC:T	donor_loss	1.0000
3:150890317:TA:T	donor_loss	1.0000
3:150890318:A:AC	donor_gain	1.0000
3:150890318:AC:A	donor_loss	1.0000
3:150890319:C:CC	donor_gain	1.0000
3:150890319:CA:C	donor_gain	1.0000
3:150890319:CACA:C	donor_gain	1.0000
3:150890319:CACAT:C	donor_gain	1.0000
3:150890394:C:CT	acceptor_gain	1.0000
3:150890936:A:AC	donor_gain	1.0000
3:150890937:C:CC	donor_gain	1.0000
3:150890937:CT:C	donor_gain	1.0000
3:150890937:CTCG:C	donor_gain	1.0000
3:150891099:ATAAG:A	acceptor_gain	1.0000
3:150891100:TAAG:T	acceptor_gain	1.0000
3:150891102:AG:A	acceptor_gain	1.0000
3:150891104:C:CC	acceptor_gain	1.0000
3:150893311:ACAGT:A	donor_gain	1.0000
3:150893312:CAGTC:C	donor_gain	1.0000
3:150893322:A:AC	donor_gain	1.0000
3:150893323:C:CC	donor_gain	1.0000
3:150894196:T:TA	donor_gain	1.0000
3:150903435:C:CT	acceptor_gain	1.0000
3:150903435:C:T	acceptor_gain	1.0000
3:150883566:T:C	acceptor_gain	0.9900

AlphaMissense

3023 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:150885394:G:C	S266R	0.990
3:150885394:G:T	S266R	0.990
3:150885396:T:G	S266R	0.990
3:150873331:A:G	W366R	0.979
3:150873331:A:T	W366R	0.979
3:150871092:A:G	W446R	0.976
3:150871092:A:T	W446R	0.976
3:150871093:C:A	K445N	0.965
3:150871093:C:G	K445N	0.965
3:150871090:C:A	W446C	0.963
3:150871090:C:G	W446C	0.963
3:150873345:G:T	P361H	0.961
3:150882946:C:T	G337D	0.960
3:150894254:A:G	W121R	0.957
3:150894254:A:T	W121R	0.957
3:150873245:A:C	F394L	0.956
3:150873245:A:T	F394L	0.956
3:150873247:A:G	F394L	0.956
3:150873354:A:G	L358P	0.949
3:150873329:C:A	W366C	0.941
3:150873329:C:G	W366C	0.941
3:150873350:C:A	K359N	0.940
3:150873350:C:G	K359N	0.940
3:150882947:C:G	G337R	0.938
3:150885392:A:G	L267P	0.933
3:150894238:A:G	F126S	0.928
3:150871091:C:G	W446S	0.923
3:150873240:A:G	L396P	0.923
3:150894252:C:A	W121C	0.923
3:150894252:C:G	W121C	0.923

dbSNP variants (sampled 300 via entrez): RS1000057775 (3:150888054 C>A), RS1000145713 (3:150897503 A>G), RS1000292313 (3:150891081 C>T), RS1000349455 (3:150905761 A>G), RS1000379210 (3:150879635 C>T), RS1000409647 (3:150899550 C>T), RS1000547173 (3:150898237 G>A), RS1000595479 (3:150889946 T>C), RS1000749602 (3:150884515 T>A), RS1000803549 (3:150893030 C>A), RS1000823391 (3:150884296 T>A), RS1000930617 (3:150904196 A>C,G), RS1001038580 (3:150901876 T>C,G), RS1001047576 (3:150896175 A>G), RS1001092923 (3:150890264 A>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aflatoxin B2	increases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.