RBMY1D

Summary

RBMY1D (RNA binding motif protein Y-linked family 1 member D, HGNC:23915) is a protein-coding gene on chromosome Yq11.223, encoding RNA-binding motif protein, Y chromosome, family 1 member D (P0C7P1). RNA-binding protein which may be involved in spermatogenesis.

This gene encodes a protein containing an RNA-binding motif in the N-terminus and four SRGY (serine, arginine, glycine, tyrosine) boxes in the C-terminus. This protein likely functions as a splicing factor during spermatogenesis. Multiple closely related paralogs of this gene are found in a gene cluster in the AZFb azoospermia factor region of chromosome Y. Most of these related copies are thought to be pseudogenes, though several likely encode functional proteins.

Source: NCBI Gene 378949 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001006120

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23915
Approved symbol	RBMY1D
Name	RNA binding motif protein Y-linked family 1 member D
Location	Yq11.223
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000244395
Ensembl biotype	protein_coding
Entrez	378949

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 nonsense_mediated_decay

ENST00000382653, ENST00000382680, ENST00000418956

RefSeq mRNA: 3 — MANE Select: NM_001006120 NM_001006120, NM_001320949, NM_001320950

CCDS: CCDS35480, CCDS83521

Canonical transcript exons

ENST00000382680 — 12 exons

Exon	Start	End
ENSE00001612685	21892405	21892517
ENSE00001636167	21894379	21894526
ENSE00001665354	21888628	21888805
ENSE00001763210	21891825	21891928
ENSE00003484557	21881064	21881152
ENSE00003489479	21882817	21882927
ENSE00003494048	21886560	21886712
ENSE00003588956	21881240	21881350
ENSE00003612403	21880076	21880652
ENSE00003646572	21883369	21883479
ENSE00003647885	21884435	21884549
ENSE00003670003	21882272	21882382

Expression profiles

Bgee: expression breadth tissue_specific, 4 present calls, max score 78.02.

Top tissues by expression

132 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	78.02	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.80	silver quality
colonic epithelium	UBERON:0000397	37.20	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
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
placenta	UBERON:0001987	33.24	gold 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
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
liver	UBERON:0002107	28.95	gold quality
right uterine tube	UBERON:0001302	28.19	gold quality
duodenum	UBERON:0002114	28.14	gold quality
ectocervix	UBERON:0012249	27.62	gold quality
lymph node	UBERON:0000029	27.57	gold quality
islet of Langerhans	UBERON:0000006	27.54	gold quality
tonsil	UBERON:0002372	27.05	gold quality
uterine cervix	UBERON:0000002	26.87	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
blood	UBERON:0000178	26.32	gold quality
leukocyte	CL:0000738	26.27	gold quality
monocyte	CL:0000576	26.14	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
muscle of leg	UBERON:0001383	25.38	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting RBMY1D, 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-3613-3P	100.00	76.36	7965
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-4777-3P	99.15	68.92	626
HSA-MIR-1843	98.97	66.07	838
HSA-MIR-4802-5P	98.97	66.26	833
HSA-MIR-6894-5P	98.70	63.78	809
HSA-MIR-6831-5P	98.26	67.20	990
HSA-MIR-509-3P	98.12	67.25	612
HSA-MIR-3927-3P	97.68	66.76	892
HSA-MIR-7154-3P	97.65	65.02	985
HSA-MIR-490-5P	96.75	65.81	661
HSA-MIR-875-5P	96.74	66.48	579

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rbmyf3	ENSMUSG00000091987
mus_musculus	Rbmyf5	ENSMUSG00000093918
mus_musculus	Rbmyf7	ENSMUSG00000093987
mus_musculus	Rbmyf6	ENSMUSG00000094511
mus_musculus	Rbmy	ENSMUSG00000094658
mus_musculus	Rbmyf2	ENSMUSG00000095852
mus_musculus	Rbmyf8	ENSMUSG00000095948
mus_musculus	Rbmyf9	ENSMUSG00000096520
mus_musculus	Rbmyf4	ENSMUSG00000101667
mus_musculus	Rbmyf1	ENSMUSG00000102053
rattus_norvegicus	Rbmy1j	ENSRNOG00000060963

Paralogs (36): DAZAP1 (ENSG00000071626), CIRBP (ENSG00000099622), RBM23 (ENSG00000100461), RBM3 (ENSG00000102317), NCL (ENSG00000115053), TIA1 (ENSG00000116001), HNRNPA2B1 (ENSG00000122566), RBM19 (ENSG00000122965), RBM39 (ENSG00000131051), MSI1 (ENSG00000135097), HNRNPA1 (ENSG00000135486), HNRNPD (ENSG00000138668), HNRNPA1L2 (ENSG00000139675), RBMX (ENSG00000147274), A1CF (ENSG00000148584), TIAL1 (ENSG00000151923), RBM46 (ENSG00000151962), HNRNPDL (ENSG00000152795), MSI2 (ENSG00000153944), RBM47 (ENSG00000163694), RBMY1F (ENSG00000169800), HNRNPA3 (ENSG00000170144), RBMXL2 (ENSG00000170748), RBM4B (ENSG00000173914), RBM4 (ENSG00000173933), RBMXL3 (ENSG00000175718), HNRNPA0 (ENSG00000177733), TRNAU1AP (ENSG00000180098), HNRNPAB (ENSG00000197451), RBMXL1 (ENSG00000213516), HNRNPA1L3 (ENSG00000224578), RBMY1J (ENSG00000226941), RBMY1A1 (ENSG00000234414), RBMY1E (ENSG00000242389), RBMY1B (ENSG00000242875), DND1 (ENSG00000256453)

Protein

Protein identifiers

RNA-binding motif protein, Y chromosome, family 1 member D — P0C7P1 (reviewed: P0C7P1)

All UniProt accessions (2): P0C7P1, F2Z2U1

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly by participating in pre-mRNA splicing in the testis.

Subunit / interactions. Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3.

Subcellular location. Nucleus.

Tissue specificity. Testis-specific.

Miscellaneous. The RBMY1 proteins are encoded by repeated regions of the Y chromosome, mostly within the AZFb region. The exact number of functional copies is unclear and may vary between individuals, and some of them may represent pseudogenes. The proteins are very similar, which makes the characterization of each protein difficult. Thus, most experiments do not discriminate between the different members. One can therefore suppose that reported interactions with a RBMY1 protein involve all the proteins.

Isoforms (2)

UniProt ID	Names	Canonical?
P0C7P1-1	1	yes
P0C7P1-2	2

RefSeq proteins (3): NP_001006120, NP_001307878, NP_001307879 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012604	RBM1CTR	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR050441	RBM	Family

Pfam: PF00076, PF08081

UniProt features (14 total): compositionally biased region 9, region of interest 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C7P1-F1	49.83	0.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): GOBP_RNA_SPLICING, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOMF_MRNA_BINDING, chrYq11, GOBP_MRNA_PROCESSING, MIR7856_5P, MIR766_5P, MIR1843, MIR4802_5P, GOCC_NUCLEAR_PROTEIN_CONTAINING_COMPLEX, FOURATI_BLOOD_TWINRIX_AGE_25_83YO_RESPONDERS_VS_POOR_RESPONDERS_0DY_DN, GOBP_MRNA_METABOLIC_PROCESS, GOBP_RNA_SPLICING_VIA_TRANSESTERIFICATION_REACTIONS

GO Biological Process (3): mRNA processing (GO:0006397), RNA splicing (GO:0008380), positive regulation of mRNA splicing, via spliceosome (GO:0048026)

GO Molecular Function (2): RNA binding (GO:0003723), nucleic acid binding (GO:0003676)

GO Cellular Component (4): nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
nuclear lumen	2
mRNA metabolic process	1
mRNA splicing, via spliceosome	1
positive regulation of RNA splicing	1
regulation of mRNA splicing, via spliceosome	1
positive regulation of mRNA processing	1
nucleic acid binding	1
binding	1
cellular anatomical structure	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
intracellular membraneless organelle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1342 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBMY1D	BPY2	O14599	800
RBMY1D	USP9Y	O00507	727
RBMY1D	CDY1	Q9Y6F8	717
RBMY1D	PRY	O14603	704
RBMY1D	UTY	O14607	697
RBMY1D	DDX3Y	O15523	676
RBMY1D	TBC1D25	Q3MII6	652
RBMY1D	KHDRBS1	Q07666	651
RBMY1D	KHDRBS3	O75525	593
RBMY1D	TSPY1	P09002	572
RBMY1D	TFE3	P19532	497
RBMY1D	KDM5D	Q9BY66	493
RBMY1D	A6NGL4	A6NGL4	479
RBMY1D	A6NGT6	A6NGT6	473
RBMY1D	REV3L	O60673	451

IntAct

0 interactions, top by confidence:

BioGRID (2): RBMY1D (Positive Genetic), RBMY1D (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1I8MUL8, A1YFA7, A2T806, A6NDE4, A6NEQ0, E9Q5K9, E9Q784, F4JCU0, O22703, O23372, O35698, O60828, O74418, O75526, P0C7P1, P0DJD3, P0DJD4, P11596, P78332, Q10B98, Q15415, Q1ECZ9, Q23935, Q24669, Q24761, Q2HJC9, Q3MHY8, Q3UC65, Q3URU2, Q3V0C1, Q4PB36, Q4R626, Q4R813, Q4R881, Q5R840, Q5T200, Q5U2S0, Q60990, Q62504, Q80Y39

Diamond homologs: A0A0A0LLY1, A2A5N3, A2VDB3, A5A6M3, A6NDE4, A6NEQ0, D4AE41, F1QB54, F4I3B3, O60176, O64380, O75526, O93235, P0C7P1, P0C8Z4, P0CB38, P0CP46, P0CP47, P0DJD3, P0DJD4, P10979, P11940, P20965, P21187, P29341, P31483, P32588, P38159, P38760, P39684, P49310, P49311, P52912, P60824, P60825, P60826, P61286, P70318, P84586, Q00539

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

4 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	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

1473 predictions. Top by Δscore:

Variant	Effect	Δscore
Y:21881057:CCCTT:C	donor_loss	1.0000
Y:21881058:CCTTA:C	donor_loss	1.0000
Y:21881059:CTTA:C	donor_loss	1.0000
Y:21881060:TTACC:T	donor_loss	1.0000
Y:21881061:TACC:T	donor_loss	1.0000
Y:21881062:A:AC	donor_gain	1.0000
Y:21881062:A:AT	donor_loss	1.0000
Y:21881063:C:CA	donor_loss	1.0000
Y:21881063:C:CC	donor_gain	1.0000
Y:21881148:GATAA:G	acceptor_gain	1.0000
Y:21881149:ATAA:A	acceptor_gain	1.0000
Y:21881150:TAA:T	acceptor_gain	1.0000
Y:21881150:TAACT:T	acceptor_loss	1.0000
Y:21881151:AA:A	acceptor_gain	1.0000
Y:21881152:ACTAA:A	acceptor_loss	1.0000
Y:21881153:C:CC	acceptor_gain	1.0000
Y:21881154:T:A	acceptor_loss	1.0000
Y:21881158:T:C	acceptor_gain	1.0000
Y:21881158:T:TC	acceptor_gain	1.0000
Y:21881242:ATAT:A	donor_gain	1.0000
Y:21882268:GTACC:G	donor_loss	1.0000
Y:21882270:A:C	donor_loss	1.0000
Y:21882271:C:A	donor_loss	1.0000
Y:21882274:ATAT:A	donor_gain	1.0000
Y:21882380:TTT:T	acceptor_gain	1.0000
Y:21882381:TT:T	acceptor_gain	1.0000
Y:21882381:TTC:T	acceptor_loss	1.0000
Y:21882382:TCTG:T	acceptor_loss	1.0000
Y:21882383:C:CA	acceptor_loss	1.0000
Y:21882383:C:CC	acceptor_gain	1.0000

AlphaMissense

3226 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
Y:21891882:A:C	F52L	1.000
Y:21891882:A:T	F52L	1.000
Y:21891884:A:G	F52L	1.000
Y:21891888:A:C	F50L	1.000
Y:21891888:A:T	F50L	1.000
Y:21891890:A:G	F50L	1.000
Y:21891873:A:C	F55L	0.999
Y:21891873:A:T	F55L	0.999
Y:21891875:A:G	F55L	0.999
Y:21891880:A:T	I53N	0.999
Y:21891883:A:G	F52S	0.999
Y:21891889:A:G	F50S	0.999
Y:21892430:A:C	F28L	0.999
Y:21892430:A:T	F28L	0.999
Y:21892432:A:G	F28L	0.999
Y:21892443:A:T	L24H	0.999
Y:21892481:G:C	F11L	0.999
Y:21892481:G:T	F11L	0.999
Y:21892482:A:G	F11S	0.999
Y:21892483:A:G	F11L	0.999
Y:21891874:A:G	F55S	0.998
Y:21891886:G:T	A51E	0.998
Y:21891894:T:A	R48S	0.998
Y:21891894:T:G	R48S	0.998
Y:21892431:A:G	F28S	0.998
Y:21892470:A:T	L15H	0.998
Y:21892479:A:T	I12N	0.998
Y:21892485:A:G	L10P	0.998
Y:21891856:G:T	A61D	0.997
Y:21891880:A:C	I53S	0.997

dbSNP variants (sampled 114 via entrez): RS112654477 (Y:21875134 A>G), RS1174227657 (Y:21890698 CG>C), RS1272313600 (Y:21901184 C>T), RS1287362844 (Y:21880645 A>T), RS1296981593 (Y:21897708 G>A), RS1326663706 (Y:21899848 C>T), RS1345833207 (Y:21880633 T>C), RS1365997383 (Y:21901330 G>T), RS1377192604 (Y:21890842 AT>A), RS1417387977 (Y:21890944 G>A), RS1430061446 (Y:21880639 A>G), RS1432414358 (Y:21901110 C>T), RS1484466042 (Y:21898471 T>C), RS1556258636 (Y:21872743 G>A), RS1556258656 (Y:21877619 G>A)

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.