GDPD4

Summary

GDPD4 (glycerophosphodiester phosphodiesterase domain containing 4, HGNC:24849) is a protein-coding gene on chromosome 11q13.5, encoding Glycerophosphodiester phosphodiesterase domain-containing protein 4 (Q6W3E5).

Predicted to enable glycerophosphodiester phosphodiesterase activity. Predicted to be involved in lipid metabolic process. Predicted to be active in membrane.

Source: NCBI Gene 220032 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 89 total
• MANE Select transcript: NM_182833

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24849
Approved symbol	GDPD4
Name	glycerophosphodiester phosphodiesterase domain containing 4
Location	11q13.5
Locus type	gene with protein product
Status	Approved
Aliases	GDE6
Ensembl gene	ENSG00000178795
Ensembl biotype	protein_coding
Entrez	220032

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 2 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000315938, ENST00000376217, ENST00000527489, ENST00000532155, ENST00000532907, ENST00000534245

RefSeq mRNA: 1 — MANE Select: NM_182833 NM_182833

CCDS: CCDS8249

Canonical transcript exons

ENST00000315938 — 17 exons

Exon	Start	End
ENSE00001216032	77227864	77227916
ENSE00001216037	77229150	77229232
ENSE00001216042	77233025	77233172
ENSE00001216047	77243694	77243848
ENSE00001216052	77245281	77245502
ENSE00001216060	77258386	77258542
ENSE00001216069	77268457	77268539
ENSE00001216076	77268924	77269069
ENSE00001216083	77269883	77269960
ENSE00001216095	77216558	77217314
ENSE00001216099	77271130	77271223
ENSE00001291846	77285085	77285187
ENSE00001313861	77279306	77279399
ENSE00003459525	77276161	77276220
ENSE00003478528	77271295	77271393
ENSE00003918644	77301605	77301686
ENSE00003919104	77287218	77287420

Expression profiles

Bgee: expression breadth ubiquitous, 115 present calls, max score 85.97.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	85.97	gold quality
left testis	UBERON:0004533	85.56	gold quality
testis	UBERON:0000473	84.58	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.97	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.89	gold quality
right lobe of liver	UBERON:0001114	69.49	gold quality
right adrenal gland cortex	UBERON:0035827	66.71	gold quality
liver	UBERON:0002107	66.63	gold quality
left adrenal gland	UBERON:0001234	66.49	gold quality
left adrenal gland cortex	UBERON:0035825	66.46	gold quality
right adrenal gland	UBERON:0001233	65.44	gold quality
adrenal gland	UBERON:0002369	65.01	gold quality
placenta	UBERON:0001987	63.76	gold quality
spleen	UBERON:0002106	55.51	gold quality
adrenal tissue	UBERON:0018303	55.00	gold quality
pituitary gland	UBERON:0000007	52.60	gold quality
metanephros cortex	UBERON:0010533	52.41	gold quality
stromal cell of endometrium	CL:0002255	51.32	silver quality
smooth muscle tissue	UBERON:0001135	50.71	gold quality
right ovary	UBERON:0002118	49.75	gold quality
ovary	UBERON:0000992	48.87	gold quality
left ovary	UBERON:0002119	48.44	gold quality
adenohypophysis	UBERON:0002196	48.16	gold quality
monocyte	CL:0000576	48.05	gold quality
skeletal muscle tissue	UBERON:0001134	47.78	silver quality
muscle tissue	UBERON:0002385	47.64	gold quality
body of pancreas	UBERON:0001150	47.56	gold quality
rectum	UBERON:0001052	47.10	gold quality
leukocyte	CL:0000738	46.85	gold quality
gall bladder	UBERON:0002110	46.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting GDPD4, 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-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-1843	98.97	66.07	838
HSA-MIR-4802-5P	98.97	66.26	833
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-6761-5P	98.71	68.03	1504
HSA-MIR-374B-3P	98.63	68.24	1360
HSA-MIR-758-3P	98.42	68.60	1122
HSA-MIR-7852-3P	98.37	67.98	823
HSA-MIR-3159	97.94	66.79	1098
HSA-MIR-483-3P	97.77	64.95	731
HSA-MIR-4708-5P	97.77	67.82	831
HSA-MIR-596	97.48	63.13	469
HSA-MIR-3157-5P	97.41	67.61	998
HSA-MIR-526B-5P	97.41	67.99	1074
HSA-MIR-1258	96.08	67.74	700

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	gdpd4b	ENSDARG00000079293
danio_rerio	gdpd4a	ENSDARG00000102447
mus_musculus	Gdpd4	ENSMUSG00000035582
rattus_norvegicus	Gdpd4	ENSRNOG00000028470

Paralogs (5): GDE1 (ENSG00000006007), GDPD3 (ENSG00000102886), GDPD2 (ENSG00000130055), GDPD1 (ENSG00000153982), GDPD5 (ENSG00000158555)

Protein

Protein identifiers

Glycerophosphodiester phosphodiesterase domain-containing protein 4 — Q6W3E5 (reviewed: Q6W3E5)

Alternative names: Glycerophosphodiester phosphodiesterase 6, UgpQ

All UniProt accessions (1): Q6W3E5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the glycerophosphoryl diester phosphodiesterase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6W3E5-1	1	yes
Q6W3E5-2	2

RefSeq proteins (1): NP_878253* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR017946	PLC-like_Pdiesterase_TIM-brl	Homologous_superfamily
IPR030395	GP_PDE_dom	Domain

Pfam: PF03009

UniProt features (26 total): topological domain 7, transmembrane region 6, sequence variant 4, binding site 3, glycosylation site 2, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6W3E5-F1	78.96	0.50

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (3): 230; 232; 245

Glycosylation sites (2): 308, 397

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 23 (showing top): chr11q13, GOBP_LIPID_METABOLIC_PROCESS, NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON, GOMF_PHOSPHORIC_DIESTER_HYDROLASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS, GOMF_PHOSPHORIC_ESTER_HYDROLASE_ACTIVITY, MIR374B_3P, MIR6851_5P, MIR3689D, MIR1843, MIR483_3P, MIR4802_5P, POU3F2_01, POU1F1_Q6, TTANTCA_UNKNOWN

GO Biological Process (1): lipid metabolic process (GO:0006629)

GO Molecular Function (4): glycerophosphodiester phosphodiesterase activity (GO:0008889), metal ion binding (GO:0046872), phosphoric diester hydrolase activity (GO:0008081), hydrolase activity (GO:0016787)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
phosphoric diester hydrolase activity	1
cation binding	1
phosphoric ester hydrolase activity	1
catalytic activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

776 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GDPD4	MECR	Q9BV79	670
GDPD4	RAB30	Q15771	454
GDPD4	GDPD3	Q7L5L3	446
GDPD4	GCDH	Q92947	444
GDPD4	AQP11	Q8NBQ7	438
GDPD4	RPS28	P25112	427
GDPD4	RET	P07949	418
GDPD4	FAM228A	Q86W67	418
GDPD4	ACER3	Q9NUN7	386
GDPD4	RBM26	Q5T8P6	382
GDPD4	METTL22	Q9BUU2	367
GDPD4	SETBP1	Q9Y6X0	365
GDPD4	FAR1	Q8WVX9	360
GDPD4	TIGD6	Q17RP2	348
GDPD4	PRUNE1	Q86TP1	344

IntAct

3 interactions, top by confidence:

A	B	Type	Score
GDPD4	KRT8	psi-mi:“MI:0915”(physical association)	0.400
GDPD4	RNF181	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (7): GDPD4 (Proximity Label-MS), RNF181 (Affinity Capture-MS), GRHPR (Cross-Linking-MS (XL-MS)), SNTB2 (Cross-Linking-MS (XL-MS)), GDPD4 (Cross-Linking-MS (XL-MS)), SNRNP200 (Cross-Linking-MS (XL-MS)), GDPD4 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2KQY6, A0A6I8PMZ8, A0JPN2, A4IGY6, A5D7L5, E9PU17, E9PX95, F1QYC4, F1S5L4, O35119, O60353, O62852, O94402, O95477, P0DX17, P41233, Q08E40, Q13433, Q15043, Q3SZN3, Q3TT99, Q4V887, Q504Y0, Q5FVQ0, Q5FWH7, Q5GJ77, Q5R9M9, Q5RAB7, Q5RCN4, Q61089, Q61586, Q6L8F3, Q6P5F6, Q6PEH9, Q6R5J1, Q6W3E5, Q75N73, Q84M24, Q8C145, Q8WMU5

Diamond homologs: A0A8F4N283, O07592, O30405, P09394, P37965, P47535, P54527, P75367, P9WLF0, P9WLF1, Q06282, Q08959, Q3T0T0, Q3TT99, Q640M6, Q6W3E5, Q7L5L3, Q8RB32, Q95JR7, Q99LY2, Q9C907, Q9ESM6, Q9HCC8, Q9JL56, Q9NZC3, Q9SD81, O14169, P10908, P9WMU2, P9WMU3, Q3KTM2, Q9JL55, P47625, Q8WTR4, P75212, Q0VGK4, Q8N9F7, Q9CRY7, Q9FGT9, Q9LVN0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	9
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2681 predictions. Top by Δscore:

Variant	Effect	Δscore
11:77258543:C:CC	acceptor_gain	1.0000
11:77268451:TCTTA:T	donor_loss	1.0000
11:77268452:CTTAC:C	donor_loss	1.0000
11:77268453:TTACC:T	donor_loss	1.0000
11:77268454:TA:T	donor_loss	1.0000
11:77268455:A:C	donor_loss	1.0000
11:77268456:C:A	donor_loss	1.0000
11:77268535:CCCAA:C	acceptor_gain	1.0000
11:77268536:CCAA:C	acceptor_gain	1.0000
11:77268536:CCAAC:C	acceptor_gain	1.0000
11:77268537:CAAC:C	acceptor_gain	1.0000
11:77258515:A:C	acceptor_gain	0.9900
11:77258540:TAA:T	acceptor_gain	0.9900
11:77258554:G:C	acceptor_gain	0.9900
11:77258554:G:GC	acceptor_gain	0.9900
11:77268455:A:AC	donor_gain	0.9900
11:77268456:C:CC	donor_gain	0.9900
11:77268537:CAA:C	acceptor_gain	0.9900
11:77268538:AA:A	acceptor_gain	0.9900
11:77268538:AACTG:A	acceptor_loss	0.9900
11:77268539:AC:A	acceptor_loss	0.9900
11:77268540:C:CC	acceptor_gain	0.9900
11:77268542:G:C	acceptor_gain	0.9900
11:77271222:ATCTG:A	acceptor_loss	0.9900
11:77271223:TC:T	acceptor_loss	0.9900
11:77271224:C:CC	acceptor_gain	0.9900
11:77271225:T:C	acceptor_loss	0.9900
11:77285076:GAAAC:G	donor_loss	0.9900
11:77285077:AAACT:A	donor_loss	0.9900
11:77285078:AACTC:A	donor_loss	0.9900

AlphaMissense

3446 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:77233102:A:G	W438R	0.988
11:77233102:A:T	W438R	0.988
11:77233100:C:A	W438C	0.984
11:77233100:C:G	W438C	0.984
11:77258524:G:C	F242L	0.981
11:77258524:G:T	F242L	0.981
11:77258526:A:G	F242L	0.981
11:77233084:A:G	S444P	0.977
11:77268503:C:G	A221P	0.977
11:77243842:A:G	W365R	0.975
11:77243842:A:T	W365R	0.975
11:77258398:A:C	F284L	0.967
11:77258398:A:T	F284L	0.967
11:77258400:A:G	F284L	0.967
11:77268525:A:C	N213K	0.964
11:77268525:A:T	N213K	0.964
11:77268955:G:T	P198Q	0.962
11:77268510:A:C	F218L	0.960
11:77268510:A:T	F218L	0.960
11:77268512:A:G	F218L	0.960
11:77243793:A:G	F381S	0.959
11:77258512:G:C	D246E	0.957
11:77258512:G:T	D246E	0.957
11:77268466:A:T	I233K	0.956
11:77268478:A:G	L229S	0.956
11:77268955:G:C	P198R	0.955
11:77268934:C:T	G205D	0.953
11:77245414:A:G	L318S	0.950
11:77258513:T:A	D246V	0.950
11:77233080:A:T	V445E	0.949

dbSNP variants (sampled 300 via entrez): RS1000027371 (11:77218983 T>C), RS1000052958 (11:77256145 T>C), RS1000076453 (11:77217822 A>G,T), RS1000123748 (11:77299297 C>T), RS1000127336 (11:77228852 A>G), RS1000155816 (11:77284524 A>G), RS1000227949 (11:77297543 A>T), RS1000251142 (11:77280415 T>A), RS1000267222 (11:77248411 C>G), RS1000332907 (11:77293956 T>C), RS1000342219 (11:77250054 T>G), RS1000355529 (11:77242695 A>G), RS1000369410 (11:77293708 C>T), RS1000389751 (11:77261092 T>G), RS1000405102 (11:77302866 C>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

1 associations (top):

Study	Trait	p-value
GCST007277_15	Tourette syndrome	5.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Atrazine	increases expression	1
Methylcholanthrene	affects binding, increases reaction	1
Tobacco Smoke Pollution	increases methylation	1

Clinical trials (associated diseases)

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