RD3L

Summary

RD3L (RD3 like, HGNC:40912) is a protein-coding gene on chromosome 14q32.33, encoding Protein RD3-like (P0DJH9).

At a glance

• GWAS associations: 5
• MANE Select transcript: NM_001257268

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40912
Approved symbol	RD3L
Name	RD3 like
Location	14q32.33
Locus type	gene with protein product
Status	Approved
Aliases	TDRD9AS1
Ensembl gene	ENSG00000227729
Ensembl biotype	protein_coding
Entrez	647286

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000557640, ENST00000648118

RefSeq mRNA: 1 — MANE Select: NM_001257268 NM_001257268

CCDS: CCDS58338

Canonical transcript exons

ENST00000557640 — 3 exons

Exon	Start	End
ENSE00001678816	103941397	103941702
ENSE00001739982	103940426	103941103
ENSE00002456459	103942092	103942529

Expression profiles

Bgee: expression breadth broad, 25 present calls, max score 84.32.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1122 / max 43.4336, expressed in 20 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
145121	0.0662	15
145122	0.0241	12
145120	0.0219	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	84.32	gold quality
heart left ventricle	UBERON:0002084	83.94	gold quality
right atrium auricular region	UBERON:0006631	80.69	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.08	gold quality
heart	UBERON:0000948	76.30	gold quality
quadriceps femoris	UBERON:0001377	70.47	gold quality
cerebellar vermis	UBERON:0004720	67.75	gold quality
thymus	UBERON:0002370	63.29	silver quality
monocyte	CL:0000576	51.59	gold quality
right lobe of liver	UBERON:0001114	51.16	gold quality
leukocyte	CL:0000738	50.16	gold quality
liver	UBERON:0002107	47.71	gold quality
skeletal muscle tissue	UBERON:0001134	41.06	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
muscle tissue	UBERON:0002385	36.73	silver 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
bone marrow	UBERON:0002371	36.08	gold quality
sural nerve	UBERON:0015488	35.99	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
muscle of leg	UBERON:0001383	35.20	gold quality
placenta	UBERON:0001987	34.82	gold quality
urinary bladder	UBERON:0001255	33.67	gold quality
gastrocnemius	UBERON:0001388	33.62	gold quality
duodenum	UBERON:0002114	32.95	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
tonsil	UBERON:0002372	32.13	gold quality
prefrontal cortex	UBERON:0000451	29.91	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	33.90
E-ANND-3	no	1.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting RD3L, 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-4500	99.99	72.72	2367
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4496	99.88	68.89	2236
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-140-5P	99.44	67.20	792
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-6769B-5P	98.73	64.91	1092
HSA-MIR-6769A-5P	97.99	64.16	851
HSA-MIR-3674	97.01	68.86	1171

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rd3l	ENSMUSG00000091402
rattus_norvegicus	Rd3l	ENSRNOG00000043031

Paralogs (1): RD3 (ENSG00000198570)

Protein

Protein identifiers

Protein RD3-like — P0DJH9 (reviewed: P0DJH9)

Alternative names: Retinal degeneration protein 3-like

All UniProt accessions (1): P0DJH9

RefSeq proteins (1): NP_001244197* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028092	RD3	Family

Pfam: PF14473

UniProt features (4 total): chain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DJH9-F1	73.41	0.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): chr14q32, YANG_BCL3_TARGETS_UP, MIR570_3P, MIR548E_5P, MIR889_3P, LET_7A_2_3P, LET_7G_3P, MIR4496, MIR202_3P, MIR3674, HAY_BONE_MARROW_PLATELET, FONG_MCMASTER_OPA1_CARDIOPROTECTION_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

278 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RD3L	C4orf46	Q504U0	631
RD3L	C3orf22	Q8N5N4	574
RD3L	BHLHA9	Q7RTU4	573
RD3L	GPR139	Q6DWJ6	541
RD3L	RRH	O14718	529
RD3L	RNASE12	Q5GAN4	528
RD3L	C12orf56	Q8IXR9	507
RD3L	DEXI	O95424	507
RD3L	SMIM17	P0DL12	507
RD3L	MAP6D1	Q9H9H5	487
RD3L	OR8D1	Q8WZ84	480
RD3L	SH2D7	A6NKC9	479
RD3L	CC2D2B	Q6DHV5	478
RD3L	C1orf167	Q5SNV9	478
RD3L	C22orf42	Q6IC83	477
RD3L	SBK3	P0C264	477

IntAct

3 interactions, top by confidence:

A	B	Type	Score
RD3L	HSPA9	psi-mi:“MI:0915”(physical association)	0.400
WRAP73	RD3L	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (1): HSPA9 (Proximity Label-MS)

ESM2 similar proteins: A2AVJ0, A6ZQU2, A6ZRI9, A6ZTA1, A7TF50, B5VQF5, C0R512, C5DN25, C7GPA7, C8ZFY3, D3Z0R2, F4IVU1, O14323, O64885, O74560, O84275, P04877, P04878, P08593, P09281, P09524, P0DJH9, P13742, P26144, P27280, P36111, P38881, P39735, P40003, P40385, P53437, P53850, Q08172, Q08270, Q0P641, Q11194, Q1HN33, Q55G18, Q5FW12, Q5RDL5

Diamond homologs: P0DJH9, Q7Z3Z2, Q8BRE0

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

138 predictions. Top by Δscore:

Variant	Effect	Δscore
14:103941099:GAAAT:G	acceptor_gain	1.0000
14:103941101:AAT:A	acceptor_gain	1.0000
14:103941102:AT:A	acceptor_gain	1.0000
14:103941102:ATCTA:A	acceptor_loss	1.0000
14:103941104:C:CC	acceptor_gain	1.0000
14:103942087:CTTA:C	donor_loss	1.0000
14:103942088:TTACC:T	donor_loss	1.0000
14:103942089:TA:T	donor_loss	1.0000
14:103942090:A:AT	donor_loss	1.0000
14:103941100:AAAT:A	acceptor_gain	0.9900
14:103942086:GCTTA:G	donor_loss	0.9900
14:103942090:A:AC	donor_gain	0.9900
14:103942091:C:CC	donor_gain	0.9900
14:103941115:A:C	acceptor_gain	0.9800
14:103942091:CCT:C	donor_gain	0.9800
14:103941102:ATCT:A	acceptor_gain	0.9700
14:103941103:TCT:T	acceptor_gain	0.9700
14:103941680:A:T	acceptor_gain	0.9700
14:103942090:AC:A	donor_gain	0.9700
14:103942091:CC:C	donor_gain	0.9700
14:103941101:AATCT:A	acceptor_gain	0.9600
14:103941104:CT:C	acceptor_gain	0.9600
14:103941105:T:A	acceptor_gain	0.9600
14:103942091:CCTG:C	donor_gain	0.9600
14:103941100:AAATC:A	acceptor_gain	0.9100
14:103941115:A:AC	acceptor_gain	0.9000
14:103941391:TTTTA:T	donor_loss	0.9000
14:103941392:TTTAC:T	donor_loss	0.9000
14:103941393:TTAC:T	donor_loss	0.9000
14:103941394:TAC:T	donor_loss	0.9000

AlphaMissense

1310 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:103941451:A:G	L82P	0.992
14:103941035:A:G	L123P	0.991
14:103941098:C:G	R102P	0.991
14:103941101:A:G	F101S	0.991
14:103941438:G:C	C86W	0.990
14:103941440:A:G	C86R	0.989
14:103941451:A:T	L82H	0.989
14:103941583:A:G	L38P	0.989
14:103941595:A:G	L34S	0.987
14:103941574:C:G	R41P	0.986
14:103941607:A:G	L30P	0.986
14:103941047:A:G	F119S	0.983
14:103941430:A:T	V89D	0.983
14:103941607:A:T	L30Q	0.981
14:103941087:C:G	A106P	0.979
14:103941439:C:T	C86Y	0.979
14:103941607:A:C	L30R	0.977
14:103941451:A:C	L82R	0.976
14:103941587:G:C	H37D	0.975
14:103940906:A:G	I166T	0.970
14:103941046:G:C	F119L	0.970
14:103941046:G:T	F119L	0.970
14:103941048:A:G	F119L	0.970
14:103941062:T:A	E114V	0.967
14:103941035:A:C	L123R	0.966
14:103941089:A:G	L105S	0.965
14:103941043:C:A	K120N	0.964
14:103941043:C:G	K120N	0.964
14:103941059:A:T	I115K	0.964
14:103941601:C:G	R32P	0.962

dbSNP variants (sampled 300 via entrez): RS1001085720 (14:103941430 A>G,T), RS1001416370 (14:103939964 T>C), RS1001451802 (14:103943006 A>G), RS1001558113 (14:103941053 T>C), RS1002172105 (14:103942974 G>A), RS1002224263 (14:103942620 T>C), RS1003178311 (14:103941328 C>A), RS1003230761 (14:103940966 T>C), RS1003951841 (14:103944468 C>G), RS1004435552 (14:103944230 G>A), RS1004514795 (14:103943502 C>T), RS1004584439 (14:103942281 T>A), RS1005025763 (14:103943904 C>T), RS1005178773 (14:103940621 A>G), RS1005625199 (14:103943325 AT>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

5 associations (top):

Study	Trait	p-value
GCST004521_262	Autism spectrum disorder or schizophrenia	6.000000e-09
GCST005951_9	Body mass index	4.000000e-09
GCST006291_63	Spherical equivalent or myopia (age of diagnosis)	2.000000e-10
GCST006803_15	Schizophrenia	3.000000e-14
GCST010002_161	Refractive error	1.000000e-20

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004847	age at onset

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
Fulvestrant	increases methylation	1

Clinical trials (associated diseases)

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