METTL25B

Summary

METTL25B (methyltransferase like 25B, HGNC:24273) is a protein-coding gene on chromosome 1q23.1, encoding Methyltransferase-like protein 25B (Q96FB5).

Predicted to enable rRNA (adenine-N6,N6-)-dimethyltransferase activity. Predicted to be involved in rRNA methylation. Predicted to be located in membrane.

Source: NCBI Gene 51093 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 99 total
• MANE Select transcript: NM_015997

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24273
Approved symbol	METTL25B
Name	methyltransferase like 25B
Location	1q23.1
Locus type	gene with protein product
Status	Approved
Aliases	CGI-41
Ensembl gene	ENSG00000143303
Ensembl biotype	protein_coding
Entrez	51093

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 16 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000368216, ENST00000368218, ENST00000462397, ENST00000476229, ENST00000481920, ENST00000484742, ENST00000497515, ENST00000517871, ENST00000519086, ENST00000522237, ENST00000524343, ENST00000892483, ENST00000892484, ENST00000892485, ENST00000892486, ENST00000917458, ENST00000917459, ENST00000917460, ENST00000917461, ENST00000917462

RefSeq mRNA: 2 — MANE Select: NM_015997 NM_001142560, NM_015997

CCDS: CCDS1154, CCDS44246

Canonical transcript exons

ENST00000368216 — 8 exons

Exon	Start	End
ENSE00000959151	156734009	156734493
ENSE00001167979	156733377	156733520
ENSE00001196007	156731991	156732115
ENSE00001446593	156728469	156729215
ENSE00003537533	156736632	156736960
ENSE00003657575	156732281	156732473
ENSE00003675907	156735725	156735909
ENSE00003678647	156732985	156733047

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 96.80.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.8055 / max 142.4192, expressed in 1807 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5762	6.6911	1758
5763	5.6592	1712
5765	3.1641	1340
5764	2.0164	1228
5766	0.2390	94
5767	0.0357	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	96.80	gold quality
right lobe of thyroid gland	UBERON:0001119	96.14	gold quality
left lobe of thyroid gland	UBERON:0001120	95.72	gold quality
right testis	UBERON:0004534	95.29	gold quality
right ovary	UBERON:0002118	95.16	gold quality
right lobe of liver	UBERON:0001114	95.13	gold quality
left ovary	UBERON:0002119	95.11	gold quality
body of pancreas	UBERON:0001150	95.07	gold quality
left testis	UBERON:0004533	94.86	gold quality
lower esophagus mucosa	UBERON:0035834	94.74	gold quality
thyroid gland	UBERON:0002046	94.65	gold quality
endocervix	UBERON:0000458	94.62	gold quality
small intestine Peyer’s patch	UBERON:0003454	94.52	gold quality
left uterine tube	UBERON:0001303	94.36	gold quality
adenohypophysis	UBERON:0002196	94.34	gold quality
ectocervix	UBERON:0012249	94.27	gold quality
body of uterus	UBERON:0009853	94.25	gold quality
body of stomach	UBERON:0001161	94.24	gold quality
mucosa of transverse colon	UBERON:0004991	94.18	gold quality
skin of abdomen	UBERON:0001416	93.92	gold quality
minor salivary gland	UBERON:0001830	93.87	gold quality
granulocyte	CL:0000094	93.81	gold quality
transverse colon	UBERON:0001157	93.72	gold quality
metanephros cortex	UBERON:0010533	93.70	gold quality
skin of leg	UBERON:0001511	93.69	gold quality
tibial nerve	UBERON:0001323	93.46	gold quality
right adrenal gland cortex	UBERON:0035827	93.17	gold quality
right adrenal gland	UBERON:0001233	93.11	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.04	gold quality
pituitary gland	UBERON:0000007	92.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting METTL25B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-10524-5P	99.05	66.08	963
HSA-MIR-4738-3P	98.98	67.98	1846
HSA-MIR-330-5P	98.73	67.63	1788
HSA-MIR-6894-5P	98.70	63.78	809
HSA-MIR-518C-5P	98.53	69.20	1640
HSA-MIR-6764-3P	98.44	67.64	1153
HSA-MIR-6824-3P	98.44	67.62	1154
HSA-MIR-3187-5P	98.36	65.74	1776
HSA-MIR-326	98.25	66.44	1565
HSA-MIR-1245B-3P	98.01	68.91	1387
HSA-MIR-10526-3P	97.86	64.97	1342
HSA-MIR-1285-3P	97.72	67.02	1932
HSA-MIR-5189-5P	97.72	66.96	1814
HSA-MIR-612	97.26	65.95	1597
HSA-MIR-6860	97.21	66.31	1656
HSA-MIR-6839-5P	96.74	68.29	1088

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	mettl25b	ENSDARG00000089033
mus_musculus	Mettl25b	ENSMUSG00000004896
rattus_norvegicus	Mettl25b	ENSRNOG00000011645
drosophila_melanogaster	CG2906	FBGN0033240
caenorhabditis_elegans	F25H2.12	WBGENE00009123

Paralogs (1): METTL25 (ENSG00000127720)

Protein

Protein identifiers

Methyltransferase-like protein 25B — Q96FB5 (reviewed: Q96FB5)

Alternative names: Protein RRNAD1, Ribosomal RNA adenine dimethylase domain-containing protein 1

All UniProt accessions (6): Q96FB5, E5RHI7, E5RI42, E5RIL6, E5RJL6, H0YBL9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the METTL25 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96FB5-1	1	yes
Q96FB5-2	2

RefSeq proteins (2): NP_001136032, NP_057081* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR020596	rRNA_Ade_Mease_Trfase_CS	Conserved_site
IPR025714	Methyltranfer_dom	Domain
IPR029063	SAM-dependent_MTases_sf	Homologous_superfamily
IPR052220	METTL25	Family

Pfam: PF13679

UniProt features (7 total): splice variant 2, chain 1, transmembrane region 1, coiled-coil region 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96FB5-F1	91.39	0.74

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 94 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_RNA_METHYLATION, GOBP_RNA_MODIFICATION, EGR1_01, HAN_SATB1_TARGETS_DN, ACEVEDO_LIVER_CANCER_UP, GOBP_RRNA_MODIFICATION, GOBP_METHYLATION, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RRNA_METHYLATION, AIYAR_COBRA1_TARGETS_UP, STAT1_02, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, MGGAAGTG_GABP_B, GOMF_RNA_METHYLTRANSFERASE_ACTIVITY

GO Biological Process (2): rRNA modification (GO:0000154), rRNA methylation (GO:0031167)

GO Molecular Function (1): rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
rRNA processing	1
RNA modification	1
rRNA modification	1
RNA methylation	1
N-methyltransferase activity	1
rRNA (adenine) methyltransferase activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

364 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
METTL25B	METTL9	Q9H1A3	530
METTL25B	CSKMT	A8MUP2	490
METTL25B	METTL13	Q8N6R0	485
METTL25B	NTMT2	Q5VVY1	484
METTL25B	METTL26	Q96S19	477
METTL25B	EEF1AKMT3	Q96AZ1	474
METTL25B	KRABD3	A5PL33	463
METTL25B	METTL27	Q8N6F8	459
METTL25B	METTL17	Q9H7H0	447
METTL25B	RSAD1	Q9HA92	444
METTL25B	EEF1AKMT2	Q5JPI9	427
METTL25B	HEATR4	Q86WZ0	419
METTL25B	TRMT44	Q8IYL2	418
METTL25B	METTL18	O95568	413
METTL25B	NRBP2	Q9NSY0	413

IntAct

2 interactions, top by confidence:

A	B	Type	Score
ERF	TBL1X	psi-mi:“MI:0914”(association)	0.530

BioGRID (4): RRNAD1 (Affinity Capture-MS), RRNAD1 (Affinity Capture-MS), RRNAD1 (Affinity Capture-MS), RRNAD1 (Affinity Capture-RNA)

ESM2 similar proteins: A2AA28, A4FV42, A4FV98, A6NDG6, D3YWP0, D3ZVU9, O15315, O35719, O70277, O75382, O94759, P21964, P57775, P81799, Q2TBS1, Q3UGX3, Q4R3I0, Q5E9V4, Q5H879, Q5RJL2, Q5SUV1, Q6DC64, Q7Z624, Q86WI3, Q86XA0, Q8BNV1, Q8C436, Q8CIW5, Q8IZ69, Q8N8L6, Q8N9F0, Q8VCX6, Q8WXB1, Q96AZ1, Q96FB5, Q96RR1, Q9BQD7, Q9BRQ3, Q9BUU2, Q9CQL0

Diamond homologs: Q5E9V4, Q6AYG0, Q8BZG5, Q96FB5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	13
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1582 predictions. Top by Δscore:

Variant	Effect	Δscore
1:156733366:C:A	acceptor_gain	1.0000
1:156733368:T:TA	acceptor_gain	1.0000
1:156733371:CTCCA:C	acceptor_loss	1.0000
1:156733372:TCCAG:T	acceptor_loss	1.0000
1:156733373:CCA:C	acceptor_loss	1.0000
1:156733374:CA:C	acceptor_loss	1.0000
1:156733375:A:AG	acceptor_gain	1.0000
1:156733375:AG:A	acceptor_gain	1.0000
1:156733376:G:GG	acceptor_gain	1.0000
1:156733376:GG:G	acceptor_gain	1.0000
1:156733376:GGGCC:G	acceptor_gain	1.0000
1:156733396:T:TA	acceptor_gain	1.0000
1:156733516:CGCAG:C	donor_loss	1.0000
1:156733517:GCAGG:G	donor_loss	1.0000
1:156733518:CAGGT:C	donor_loss	1.0000
1:156733522:T:G	donor_loss	1.0000
1:156735903:G:GT	donor_gain	1.0000
1:156735908:GG:G	donor_gain	1.0000
1:156735909:GG:G	donor_gain	1.0000
1:156729216:G:GG	donor_gain	0.9900
1:156729227:GGGGC:G	donor_gain	0.9900
1:156729228:GGGCG:G	donor_gain	0.9900
1:156729229:G:T	donor_gain	0.9900
1:156732039:G:GT	donor_gain	0.9900
1:156732983:A:AG	acceptor_gain	0.9900
1:156732983:AGTT:A	acceptor_gain	0.9900
1:156732984:G:GG	acceptor_gain	0.9900
1:156732984:GTT:G	acceptor_gain	0.9900
1:156732984:GTTG:G	acceptor_gain	0.9900
1:156733376:GGGC:G	acceptor_gain	0.9900

AlphaMissense

3014 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:156736680:G:T	R452I	0.998
1:156732446:G:C	K134N	0.997
1:156732446:G:T	K134N	0.997
1:156732455:G:C	E137D	0.997
1:156732455:G:T	E137D	0.997
1:156736680:G:C	R452T	0.997
1:156732433:T:A	V130D	0.996
1:156734144:C:G	H258D	0.996
1:156736658:T:C	F445L	0.996
1:156736660:C:A	F445L	0.996
1:156736660:C:G	F445L	0.996
1:156732454:A:T	E137V	0.995
1:156735865:A:T	E421V	0.995
1:156736681:A:C	R452S	0.995
1:156736681:A:T	R452S	0.995
1:156733425:A:C	S181R	0.994
1:156733427:C:A	S181R	0.994
1:156733427:C:G	S181R	0.994
1:156732443:G:C	K133N	0.993
1:156732443:G:T	K133N	0.993
1:156732444:A:G	K134E	0.993
1:156734225:T:C	C285R	0.993
1:156735883:A:T	D427V	0.993
1:156734146:C:A	H258Q	0.992
1:156734146:C:G	H258Q	0.992
1:156734154:G:T	G261V	0.992
1:156735886:G:C	R428P	0.992
1:156731994:T:C	F39L	0.991
1:156731996:T:A	F39L	0.991
1:156731996:T:G	F39L	0.991

dbSNP variants (sampled 300 via entrez): RS1000265049 (1:156735212 C>A,G), RS1000402548 (1:156731851 G>T), RS1000456130 (1:156731518 G>T), RS1000639299 (1:156734891 T>C), RS1001183087 (1:156729224 A>G), RS1001387632 (1:156733342 G>A,T), RS1001439893 (1:156732964 C>A,T), RS1001537087 (1:156729292 G>A,T), RS1001609278 (1:156729531 T>C), RS1002386765 (1:156728244 C>A,T), RS1002391850 (1:156734754 A>G,T), RS1002747236 (1:156728529 C>A,T), RS1003220980 (1:156730539 C>T), RS1003293153 (1:156730815 C>T), RS1003801619 (1:156729405 CTTTT>C,CTT,CTTT,CTTTTT,CTTTTTT,CTTTTTTTTTTT)

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

1 associations (top):

Study	Trait	p-value
GCST010002_368	Refractive error	7.000000e-38

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
abrine	increases expression	1
(+)-JQ1 compound	increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Estradiol	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Smoke	decreases expression	1
Tunicamycin	increases expression	1
Valproic Acid	decreases expression	1
Cyclosporine	increases expression	1
Okadaic Acid	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TJ79	HAP1 RRNAD1 (-) 1	Cancer cell line	Male
CVCL_XS30	HAP1 RRNAD1 (-) 2	Cancer cell line	Male
CVCL_XS31	HAP1 RRNAD1 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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