RAMACL

Summary

RAMACL (RNA guanine-7 methyltransferase activating subunit like, HGNC:21234) is a protein-coding gene on chromosome 6q27, encoding RNA guanine-N7 methyltransferase-activating subunit-like protein (A0A3B3IU46). Component of the mRNA-capping methyltransferase RNMT:RAMAC complex that methylates the N7 position of the added guanosine to the 5’-cap structure of mRNAs.

Predicted to enable RNA binding activity. Predicted to be involved in RNA 5’-cap (guanine-N7)-methylation. Predicted to be located in nucleus. Predicted to be part of mRNA capping enzyme complex.

Source: NCBI Gene 353267 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001395999

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21234
Approved symbol	RAMACL
Name	RNA guanine-7 methyltransferase activating subunit like
Location	6q27
Locus type	gene with protein product
Status	Approved
Aliases	dJ427A4.2
Ensembl gene	ENSG00000235272
Ensembl biotype	protein_coding
Entrez	353267

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000444122

RefSeq mRNA: 1 — MANE Select: NM_001395999 NM_001395999

CCDS: CCDS94031

Canonical transcript exons

ENST00000444122 — 1 exons

Exon	Start	End
ENSE00003978321	166583009	166586678

Expression profiles

Bgee: expression breadth ubiquitous, 116 present calls, max score 79.89.

Top tissues by expression

128 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	79.89	gold quality
corpus callosum	UBERON:0002336	59.72	gold quality
bone marrow cell	CL:0002092	58.99	silver quality
subcutaneous adipose tissue	UBERON:0002190	58.15	gold quality
bone marrow	UBERON:0002371	56.95	gold quality
colonic epithelium	UBERON:0000397	56.85	gold quality
sural nerve	UBERON:0015488	55.96	silver quality
stromal cell of endometrium	CL:0002255	54.25	gold quality
upper lobe of left lung	UBERON:0008952	53.73	gold quality
skin of leg	UBERON:0001511	52.82	gold quality
adipose tissue	UBERON:0001013	52.13	gold quality
skeletal muscle tissue	UBERON:0001134	51.64	gold quality
lung	UBERON:0002048	51.59	gold quality
tonsil	UBERON:0002372	51.11	silver quality
zone of skin	UBERON:0000014	51.00	gold quality
calcaneal tendon	UBERON:0003701	50.98	silver quality
left uterine tube	UBERON:0001303	50.95	gold quality
tibial nerve	UBERON:0001323	50.76	gold quality
right coronary artery	UBERON:0001625	50.41	gold quality
uterine cervix	UBERON:0000002	49.99	gold quality
thoracic mammary gland	UBERON:0005200	49.40	gold quality
mucosa of stomach	UBERON:0001199	48.79	gold quality
urinary bladder	UBERON:0001255	48.59	gold quality
skin of abdomen	UBERON:0001416	48.27	gold quality
gastrocnemius	UBERON:0001388	48.12	gold quality
ectocervix	UBERON:0012249	47.52	gold quality
right lobe of thyroid gland	UBERON:0001119	47.30	gold quality
muscle of leg	UBERON:0001383	47.04	gold quality
body of uterus	UBERON:0009853	46.95	gold quality
vagina	UBERON:0000996	46.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.22

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ramac	ENSMUSG00000038646
mus_musculus	Ramacl	ENSMUSG00000074826
rattus_norvegicus	Ramac	ENSRNOG00000019426

Paralogs (1): RAMAC (ENSG00000169612)

Protein

Protein identifiers

RNA guanine-N7 methyltransferase-activating subunit-like protein — A0A3B3IU46 (reviewed: A0A3B3IU46)

All UniProt accessions (1): A0A3B3IU46

UniProt curated annotations — full annotation on UniProt →

Function. Component of the mRNA-capping methyltransferase RNMT:RAMAC complex that methylates the N7 position of the added guanosine to the 5’-cap structure of mRNAs.

Subunit / interactions. Interacts with RNMT.

Subcellular location. Nucleus.

Similarity. Belongs to the RAM family.

RefSeq proteins (1): NP_001382928* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028271	RAMAC	Family

Pfam: PF15320

UniProt features (7 total): compositionally biased region 4, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A3B3IU46-F1	61.82	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 20 (showing top): GOBP_RNA_METHYLATION, GOBP_RNA_MODIFICATION, GOBP_RNA_CAPPING, chr6q27, GOBP_METHYLATION, GOMF_ENZYME_ACTIVATOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY, GOBP_RNA_5_END_PROCESSING, GOBP_RNA_GUANINE_N7_METHYLATION, GOBP_MRNA_PROCESSING, ZFP91_TARGET_GENES, ZNF407_TARGET_GENES, ZNF507_TARGET_GENES, GOCC_NUCLEAR_PROTEIN_CONTAINING_COMPLEX, GOMF_MOLECULAR_FUNCTION_ACTIVATOR_ACTIVITY

GO Biological Process (1): RNA 5’-cap (guanine-N7)-methylation (GO:0106005)

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (2): mRNA capping enzyme complex (GO:0031533), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
7-methylguanosine RNA capping	1
RNA (guanine-N7)-methylation	1
nucleic acid binding	1
nuclear protein-containing complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

392 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAMACL	RNMT	O43148	337
RAMACL	SETX	Q7Z333	285
RAMACL	CSTF3	Q12996	261
RAMACL	TMEM242	Q9NWH2	259
RAMACL	PCF11	O94913	256
RAMACL	SERAC1	Q96JX3	249
RAMACL	XRN2	Q9H0D6	245
RAMACL	TULP4	Q9NRJ4	237
RAMACL	ELOF1	P60002	220
RAMACL	WDR12	Q9GZL7	202
RAMACL	PSPH	P78330	187
RAMACL	URB1	O60287	177
RAMACL	TMEM196	Q5HYL7	176
RAMACL	EXOSC10	Q01780	166
RAMACL	LETM1	O95202	164
RAMACL	RNGTT	O60942	164

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A3B3IU46, A0JMU8, A1L1K8, A2RV70, O94432, P07733, P45978, P46553, P90897, Q09801, Q09911, Q14444, Q1LZB6, Q24669, Q28F29, Q28HC9, Q2HJG4, Q5CZI8, Q5JVS0, Q5M9G3, Q5R9Q6, Q5UR41, Q5ZMS6, Q60865, Q66HC1, Q6CVS3, Q6FJC7, Q6NRP6, Q6NRY1, Q6NYG6, Q6P0F4, Q6P1U3, Q75A59, Q8CGZ0, Q8IWX8, Q8TAP9, Q8VDM6, Q91W18, Q9BTL3, Q9BUJ2

Diamond homologs: A0A3B3IU46, Q28HC9, Q5R9Q6, Q9BTL3, Q9CQY2

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

48 predictions. Top by Δscore:

Variant	Effect	Δscore
6:166583862:TAATG:T	acceptor_gain	0.7600
6:166586127:G:C	donor_gain	0.5900
6:166583864:ATGGT:A	acceptor_gain	0.5700
6:166583698:CAAGA:C	donor_gain	0.4900
6:166583875:GGTT:G	acceptor_gain	0.4900
6:166583874:AGGTT:A	acceptor_gain	0.4600
6:166583834:A:T	acceptor_gain	0.4500
6:166584406:A:C	acceptor_gain	0.4400
6:166583863:AATGG:A	acceptor_gain	0.4000
6:166583097:T:A	acceptor_gain	0.3900
6:166583697:A:AC	donor_gain	0.3900
6:166583698:C:CC	donor_gain	0.3900
6:166586485:ATCCC:A	acceptor_gain	0.3500
6:166583857:CTAT:C	acceptor_gain	0.3300
6:166584395:CAAA:C	acceptor_gain	0.3200
6:166585042:TTGC:T	donor_gain	0.3200
6:166586484:AATCC:A	acceptor_gain	0.3100
6:166583877:T:A	acceptor_gain	0.3000
6:166583305:TGC:T	donor_gain	0.2900
6:166583785:C:CC	acceptor_gain	0.2900
6:166583843:TA:T	acceptor_gain	0.2900
6:166583784:A:AC	acceptor_gain	0.2800
6:166583842:TTA:T	acceptor_gain	0.2800
6:166583868:T:A	acceptor_gain	0.2800
6:166583876:GTT:G	acceptor_gain	0.2800
6:166583858:T:G	acceptor_gain	0.2700
6:166583859:ATC:A	acceptor_gain	0.2700
6:166583860:TCT:T	acceptor_gain	0.2700
6:166583872:A:C	acceptor_gain	0.2700
6:166583079:T:TC	acceptor_gain	0.2600

AlphaMissense

781 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:166586421:G:C	F19L	0.977
6:166586421:G:T	F19L	0.977
6:166586423:A:G	F19L	0.977
6:166586433:A:C	F15L	0.977
6:166586433:A:T	F15L	0.977
6:166586435:A:G	F15L	0.977
6:166586401:T:G	Y26S	0.974
6:166586402:A:C	Y26D	0.966
6:166586351:A:G	W43R	0.961
6:166586351:A:T	W43R	0.961
6:166586422:A:G	F19S	0.955
6:166586402:A:T	Y26N	0.938
6:166586402:A:G	Y26H	0.935
6:166586349:C:A	W43C	0.927
6:166586349:C:G	W43C	0.927
6:166586434:A:G	F15S	0.919
6:166586410:T:A	D23V	0.911
6:166586389:A:G	L30P	0.904
6:166586434:A:C	F15C	0.899
6:166586401:T:C	Y26C	0.890
6:166586424:T:A	R18S	0.888
6:166586424:T:G	R18S	0.888
6:166586445:A:C	F11L	0.888
6:166586445:A:T	F11L	0.888
6:166586447:A:G	F11L	0.888
6:166586410:T:G	D23A	0.883
6:166586411:C:G	D23H	0.883
6:166586435:A:T	F15I	0.880
6:166586359:A:T	V40D	0.879
6:166586422:A:C	F19C	0.856

dbSNP variants (sampled 300 via entrez): RS1000589372 (6:166584727 C>T), RS1000682593 (6:166584975 C>G), RS1000728378 (6:166583729 A>C), RS1002055764 (6:166584528 A>G,T), RS1002132938 (6:166583992 T>C), RS1002149093 (6:166584784 C>A,T), RS1002728157 (6:166588260 G>A), RS1002738083 (6:166588479 C>T), RS1003825004 (6:166587025 C>T), RS1004056626 (6:166588165 T>C), RS1004087589 (6:166587859 C>G,T), RS1004217220 (6:166582570 A>C,G,T), RS1006329446 (6:166584541 C>G), RS1007058497 (6:166585030 T>C,G), RS1007141146 (6:166587681 C>A,T)

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.