MBD3L2B

Summary

MBD3L2B (methyl-CpG binding domain protein 3 like 2B, HGNC:53435) is a protein-coding gene on chromosome 19p13.2, encoding Methyl-CpG-binding domain protein 3-like 2B (A0A1B0GVZ6).

Predicted to enable methyl-CpG binding activity. Predicted to be involved in DNA methylation-dependent constitutive heterochromatin formation and negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 729458 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001364674

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53435
Approved symbol	MBD3L2B
Name	methyl-CpG binding domain protein 3 like 2B
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000196589
Ensembl biotype	protein_coding
Entrez	729458

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000636986

RefSeq mRNA: 1 — MANE Select: NM_001364674 NM_001364674

CCDS: CCDS92501

Canonical transcript exons

ENST00000636986 — 2 exons

Exon	Start	End
ENSE00003799490	7018969	7019730
ENSE00003799921	7021353	7021431

Expression profiles

Bgee: expression breadth tissue_specific, 7 present calls, max score 50.67.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	50.67	silver quality
ganglionic eminence	UBERON:0004023	37.69	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
sural nerve	UBERON:0015488	36.73	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
right testis	UBERON:0004534	34.03	silver quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
left testis	UBERON:0004533	32.73	silver quality
testis	UBERON:0000473	32.50	silver quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
monocyte	CL:0000576	30.17	gold quality
leukocyte	CL:0000738	29.94	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
liver	UBERON:0002107	28.99	gold quality
duodenum	UBERON:0002114	28.14	gold quality
primary visual cortex	UBERON:0002436	28.02	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
blood	UBERON:0000178	26.60	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
cortex of kidney	UBERON:0001225	26.00	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
right lobe of liver	UBERON:0001114	24.81	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-36552	yes	688.82
E-MTAB-10018	yes	380.51
E-ANND-3	no	0.66

Regulation

Is transcription factor: no

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	mbd3a	ENSDARG00000061774
mus_musculus	Mbd3l2	ENSMUSG00000047508
rattus_norvegicus	Mbd3l2	ENSRNOG00000026629
rattus_norvegicus	Mbd3l3	ENSRNOG00000065634
drosophila_melanogaster	MBD-like	FBGN0027950

Paralogs (8): MBD3 (ENSG00000071655), MBD2 (ENSG00000134046), MBD1 (ENSG00000141644), MBD3L1 (ENSG00000170948), MBD3L3 (ENSG00000182315), MBD3L4 (ENSG00000205718), MBD3L2 (ENSG00000230522), MBD3L5 (ENSG00000237247)

Protein

Protein identifiers

Methyl-CpG-binding domain protein 3-like 2B — A0A1B0GVZ6 (reviewed: A0A1B0GVZ6)

All UniProt accessions (1): A0A1B0GVZ6

UniProt curated annotations — full annotation on UniProt →

Miscellaneous. The MBD3L proteins are encoded by strongly repeated regions of the 19p13 chromosome. The exact number of functional copies is unclear, and some of them may represent pseudogenes.

Similarity. Belongs to the MBD3L family.

RefSeq proteins (1): NP_001351603* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025884	MeCpG-bd_2/3_C_dom	Domain
IPR032343	MBD2/MBD3_p55-bd	Domain

Pfam: PF14048, PF16564

UniProt features (3 total): chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GVZ6-F1	66.14	0.17

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 14 (showing top): GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, GOBP_DNA_METHYLATION_DEPENDENT_CONSTITUTIVE_HETEROCHROMATIN_FORMATION, GOBP_CHROMATIN_REMODELING, GOBP_HETEROCHROMATIN_ORGANIZATION, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, chr19p13, GOMF_METHYL_CPG_BINDING, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION, GOBP_CONSTITUTIVE_HETEROCHROMATIN_FORMATION, GOBP_CHROMATIN_ORGANIZATION, GOBP_NEGATIVE_REGULATION_OF_RNA_BIOSYNTHETIC_PROCESS

GO Biological Process (2): negative regulation of transcription by RNA polymerase II (GO:0000122), DNA methylation-dependent constitutive heterochromatin formation (GO:0006346)

GO Molecular Function (1): methyl-CpG binding (GO:0008327)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
constitutive heterochromatin formation	1
nucleotide binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GVZ6, A5D7I0, A6H7B4, A6NDZ8, A6NE82, A6NJ08, A6NJB7, A6NJI1, A6NL46, A6QP24, A8MUA0, A8MUI8, A8MV72, A8MX80, B2RW88, O94850, P0C6A0, P24097, P50617, Q0P5M0, Q0VD86, Q2KIL8, Q3B8N5, Q3SY00, Q3SYA9, Q3UN58, Q5BMD4, Q5JTZ5, Q5RBE4, Q5VZ46, Q66MI6, Q68US1, Q6GQV0, Q6PAC4, Q80TS7, Q80VY2, Q8BFY7, Q8BII1, Q8IXW0, Q8K2F3

Diamond homologs: A0A1B0GVZ6, A6NDZ8, A6NE82, A6NJ08, O95983, Q8NHZ7, Q8WWY6, Q9D9H3, Q9UBB5, Q9Z2D8, Q9Z2E1, O95243, P51608, Q00566, Q95LG8, Q9UIS9, Q9Z2D6, Q9Z2D7, Q9Z2E2, Q9FZP6, Q9LTJ1, Q9LYB9

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

0 predictions. Top by Δscore:

AlphaMissense

1310 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:7019605:G:C	F57L	0.963
19:7019605:G:T	F57L	0.963
19:7019607:A:G	F57L	0.963
19:7019614:G:C	S54R	0.921
19:7019614:G:T	S54R	0.921
19:7019616:T:G	S54R	0.921
19:7019218:C:A	R186S	0.920
19:7019218:C:G	R186S	0.920
19:7019618:G:A	T53I	0.916
19:7019242:C:A	Q178H	0.901
19:7019242:C:G	Q178H	0.901
19:7019606:A:G	F57S	0.901
19:7019219:C:A	R186M	0.895
19:7019591:G:A	T62I	0.877
19:7019585:A:G	I64T	0.870
19:7019606:A:C	F57C	0.866
19:7019623:T:A	R51S	0.850
19:7019623:T:G	R51S	0.850
19:7019223:C:G	A185P	0.841
19:7019202:C:G	A192P	0.838
19:7019518:T:A	Q86H	0.836
19:7019518:T:G	Q86H	0.836
19:7019219:C:G	R186T	0.833
19:7019609:A:G	I56T	0.829
19:7019708:A:G	M23T	0.828
19:7019615:C:A	S54I	0.826
19:7019607:A:C	F57V	0.811
19:7019607:A:T	F57I	0.810
19:7019198:A:G	L193S	0.800
19:7019585:A:C	I64S	0.799

dbSNP variants (sampled 300 via entrez): RS1001182387 (19:7019080 T>C), RS1005662923 (19:7018825 AACAAG>A), RS1009858425 (19:7018545 C>T), RS1011459337 (19:7019101 A>C,G), RS1011947348 (19:7019944 G>C), RS1015736417 (19:7018593 G>A), RS1016640587 (19:7019156 A>C,G), RS1017088463 (19:7018742 C>A,G,T), RS1019219635 (19:7018633 C>T), RS1020194683 (19:7020138 C>G), RS1020539383 (19:7019102 C>T), RS1024393348 (19:7018877 G>A), RS1027859982 (19:7018614 T>C), RS1028459010 (19:7018707 A>C), RS1030098642 (19:7020230 T>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)

Clinical trials (associated diseases)

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