WDR38

Summary

WDR38 (WD repeat domain 38, HGNC:23745) is a protein-coding gene on chromosome 9q33.3, encoding WD repeat-containing protein 38 (Q5JTN6).

Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of transferase complex.

Source: NCBI Gene 401551 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 72 total
• MANE Select transcript: NM_001045476

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23745
Approved symbol	WDR38
Name	WD repeat domain 38
Location	9q33.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000136918
Ensembl biotype	protein_coding
Entrez	401551

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000373574, ENST00000613760, ENST00000618744, ENST00000862300, ENST00000862301, ENST00000862302, ENST00000862303, ENST00000862304, ENST00000862305, ENST00000945323, ENST00000945324

RefSeq mRNA: 4 — MANE Select: NM_001045476 NM_001045476, NM_001276374, NM_001276375, NM_001276376

CCDS: CCDS43876, CCDS75898, CCDS75899

Canonical transcript exons

ENST00000373574 — 9 exons

Exon	Start	End
ENSE00000806662	124856732	124856881
ENSE00000806665	124855861	124855958
ENSE00000983705	124854205	124854325
ENSE00001036144	124857364	124857411
ENSE00001091371	124856240	124856320
ENSE00001155644	124856469	124856600
ENSE00001298449	124855634	124855750
ENSE00001460935	124857502	124857878
ENSE00001460940	124853460	124853600

Expression profiles

Bgee: expression breadth broad, 100 present calls, max score 98.44.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2066 / max 49.8153, expressed in 67 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98487	0.1420	56
98486	0.0646	35

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	98.44	gold quality
right uterine tube	UBERON:0001302	98.12	gold quality
bronchus	UBERON:0002185	97.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.25	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.29	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.70	gold quality
nasal cavity epithelium	UBERON:0005384	86.31	gold quality
oviduct epithelium	UBERON:0004804	84.06	gold quality
fallopian tube	UBERON:0003889	83.41	gold quality
sperm	CL:0000019	81.20	silver quality
epithelium of nasopharynx	UBERON:0001951	80.94	gold quality
nasal cavity mucosa	UBERON:0001826	79.08	gold quality
oocyte	CL:0000023	76.08	gold quality
caput epididymis	UBERON:0004358	73.09	gold quality
tendon of biceps brachii	UBERON:0008188	72.60	silver quality
trachea	UBERON:0003126	72.51	gold quality
right testis	UBERON:0004534	72.43	gold quality
left testis	UBERON:0004533	70.77	gold quality
right lung	UBERON:0002167	68.98	gold quality
testis	UBERON:0000473	68.93	gold quality
buccal mucosa cell	CL:0002336	68.60	gold quality
left uterine tube	UBERON:0001303	68.20	gold quality
secondary oocyte	CL:0000655	67.69	gold quality
endothelial cell	CL:0000115	67.24	gold quality
vastus lateralis	UBERON:0001379	66.81	gold quality
upper arm skin	UBERON:0004263	66.49	gold quality
quadriceps femoris	UBERON:0001377	66.36	gold quality
superficial temporal artery	UBERON:0001614	66.11	gold quality
cardiac muscle of right atrium	UBERON:0003379	65.24	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	64.84	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	26.95
E-MTAB-10287	yes	26.67
E-ANND-3	yes	10.25

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting WDR38, 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-6756-5P	99.82	67.97	2466
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-363-5P	99.46	64.51	1015
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-181A-2-3P	98.91	67.60	1168
HSA-MIR-6769B-5P	98.73	64.91	1092
HSA-MIR-6509-3P	98.32	67.33	1343
HSA-MIR-6810-5P	98.29	66.21	975
HSA-MIR-4701-3P	98.17	66.25	788
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-6769A-5P	97.99	64.16	851
HSA-MIR-3144-5P	97.64	65.45	646
HSA-MIR-4456	97.50	64.88	1678
HSA-MIR-4288	97.11	67.23	1636
HSA-MIR-873-3P	96.84	66.09	786
HSA-MIR-632	96.08	67.17	798
HSA-MIR-6741-5P	93.86	63.06	437

Literature-anchored findings (GeneRIF, showing 1)

• WDR38, a novel equatorial segment protein, interacts with the GTPase protein RAB19 and Golgi protein GM130 to play roles in acrosome biogenesis. (PMID:37635409)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Wdr38	ENSMUSG00000035295
rattus_norvegicus	Wdr38	ENSRNOG00000014102

Paralogs (26): PAFAH1B1 (ENSG00000007168), SNRNP40 (ENSG00000060688), WDR62 (ENSG00000075702), WDR7 (ENSG00000091157), TBL2 (ENSG00000106638), PAK1IP1 (ENSG00000111845), WDR75 (ENSG00000115368), DCAF4 (ENSG00000119599), DAW1 (ENSG00000123977), TEP1 (ENSG00000129566), AHI1 (ENSG00000135541), MAPKBP1 (ENSG00000137802), POC1B (ENSG00000139323), NEDD1 (ENSG00000139350), COP1 (ENSG00000143207), WDR17 (ENSG00000150627), WDR43 (ENSG00000163811), POC1A (ENSG00000164087), WDR88 (ENSG00000166359), WDR81 (ENSG00000167716), DCAF4L2 (ENSG00000176566), DCAF4L1 (ENSG00000182308), WDR27 (ENSG00000184465), NWD1 (ENSG00000188039), WDR5 (ENSG00000196363), WDR5B (ENSG00000196981)

Protein

Protein identifiers

WD repeat-containing protein 38 — Q5JTN6 (reviewed: Q5JTN6)

All UniProt accessions (3): A0A087X0D8, A0A087X0J1, Q5JTN6

RefSeq proteins (4): NP_001038941, NP_001263303, NP_001263304, NP_001263305 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR019775	WD40_repeat_CS	Conserved_site
IPR020472	WD40_PAC1	Repeat
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily

Pfam: PF00400

UniProt features (11 total): repeat 7, sequence variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JTN6-F1	87.65	0.68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 45 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOCC_TRANSFERASE_COMPLEX, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, MARTENS_TRETINOIN_RESPONSE_DN, HHEX_TARGET_GENES, HOXC6_TARGET_GENES, IGLV5_37_TARGET_GENES, ZNF282_TARGET_GENES, ZNF322_TARGET_GENES, ZNF92_TARGET_GENES, ZSCAN31_TARGET_GENES, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2

GO Biological Process (1): hematopoietic progenitor cell differentiation (GO:0002244)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): transferase complex (GO:1990234)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
hemopoiesis	1
cell differentiation	1
binding	1
catalytic complex	1

Protein interactions and networks

STRING

1396 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR38	OR1Q1	Q15612	581
WDR38	OR51I2	Q9H344	492
WDR38	KNOP1	Q1ED39	483
WDR38	FAM133B	Q5BKY9	443
WDR38	GARIN2	Q8N9W8	439
WDR38	OR2H1	Q9GZK4	428
WDR38	ANKK1	Q8NFD2	426
WDR38	IGSF6	O95976	396
WDR38	DEPP1	Q9NTK1	393
WDR38	ZNF750	Q32MQ0	391
WDR38	ACCSL	Q4AC99	381
WDR38	ANKRD36B	Q8N2N9	371
WDR38	VWA3A	A6NCI4	368
WDR38	LRRC24	Q50LG9	364
WDR38	SLC15A5	A6NIM6	363
WDR38	FAM163A	Q96GL9	363

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0AUS0, A8XXC7, B3RQN1, B6K7R8, C5DF48, E9Q4P1, F4INY4, G5EEG7, O74453, O94394, P38123, P62883, P62884, Q18964, Q25306, Q2KIY3, Q2TAY7, Q2TBS9, Q38SD2, Q3EBD3, Q3MKM6, Q3UHC2, Q3UKJ7, Q5FVN8, Q5JTN6, Q5ZMC3, Q5ZME8, Q67UX0, Q6C953, Q6NRT3, Q6TNS2, Q76B40, Q7ZVA0, Q8BUB4, Q8H594, Q8IWB7, Q8N9V3, Q8SRB0, Q8W117, Q91WQ5

Diamond homologs: Q5JTN6, Q9D994, P07834, Q54PE0, Q86TI4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1679 predictions. Top by Δscore:

Variant	Effect	Δscore
9:124853598:G:GT	donor_gain	1.0000
9:124853598:G:T	donor_gain	1.0000
9:124854404:A:G	donor_gain	1.0000
9:124855749:GG:G	donor_gain	1.0000
9:124855849:T:A	acceptor_gain	1.0000
9:124856598:CTGG:C	donor_loss	1.0000
9:124856599:TGGTA:T	donor_loss	1.0000
9:124856601:G:C	donor_loss	1.0000
9:124856601:G:GG	donor_gain	1.0000
9:124856602:T:G	donor_loss	1.0000
9:124857362:A:AG	acceptor_gain	1.0000
9:124857362:AGGT:A	acceptor_loss	1.0000
9:124857363:G:GG	acceptor_gain	1.0000
9:124858066:CC:C	acceptor_gain	1.0000
9:124858066:CCCTG:C	acceptor_loss	1.0000
9:124858067:CC:C	acceptor_gain	1.0000
9:124858068:C:CA	acceptor_loss	1.0000
9:124858069:T:A	acceptor_loss	1.0000
9:124853568:A:T	donor_gain	0.9900
9:124853600:GGTGA:G	donor_loss	0.9900
9:124853601:GTGAG:G	donor_loss	0.9900
9:124853602:T:G	donor_loss	0.9900
9:124854228:T:TA	acceptor_gain	0.9900
9:124854309:GC:G	donor_gain	0.9900
9:124854324:AGG:A	donor_loss	0.9900
9:124854326:G:GC	donor_loss	0.9900
9:124854327:T:G	donor_loss	0.9900
9:124854409:C:G	donor_gain	0.9900
9:124854414:C:T	donor_gain	0.9900
9:124855631:CAG:C	acceptor_loss	0.9900

AlphaMissense

2035 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:124855681:A:C	S80R	0.997
9:124855683:C:A	S80R	0.997
9:124855683:C:G	S80R	0.997
9:124856861:A:C	S250R	0.994
9:124856863:C:A	S250R	0.994
9:124856863:C:G	S250R	0.994
9:124855890:T:C	F113L	0.984
9:124855892:C:A	F113L	0.984
9:124855892:C:G	F113L	0.984
9:124855679:C:A	A79D	0.983
9:124855694:A:T	D84V	0.980
9:124857375:G:C	W260C	0.980
9:124857375:G:T	W260C	0.980
9:124855930:A:T	D126V	0.979
9:124854279:G:C	W48C	0.978
9:124854279:G:T	W48C	0.978
9:124856739:G:A	G209D	0.977
9:124855929:G:C	D126H	0.976
9:124855703:T:A	V87D	0.975
9:124855706:G:C	R88P	0.975
9:124855711:T:A	W90R	0.975
9:124855711:T:C	W90R	0.975
9:124856747:G:C	D212H	0.975
9:124857373:T:A	W260R	0.975
9:124857373:T:C	W260R	0.975
9:124855713:G:C	W90C	0.974
9:124855713:G:T	W90C	0.974
9:124856476:G:A	G165D	0.974
9:124856568:A:C	S196R	0.974
9:124856570:C:A	S196R	0.974

dbSNP variants (sampled 300 via entrez): RS1001774536 (9:124857230 G>A), RS1002575809 (9:124852809 G>A), RS1002772779 (9:124856020 A>C,T), RS1003489784 (9:124853513 G>A), RS1004131146 (9:124856205 C>A,G), RS1004896655 (9:124852339 C>T), RS1004926269 (9:124854529 C>T), RS1005167952 (9:124854685 T>A), RS1005173996 (9:124854477 T>G), RS1005577543 (9:124857541 G>A,C,T), RS1005811799 (9:124851928 G>A), RS1005906769 (9:124852056 C>T), RS1006591728 (9:124854605 G>A), RS1007912396 (9:124858212 C>T), RS1008200374 (9:124855551 G>C)

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)

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, decreases methylation	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	increases methylation	1
tebuconazole	decreases expression	1
licochalcone B	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Resveratrol	decreases expression, affects cotreatment	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	increases abundance, increases expression	1
Cadmium	decreases expression, increases abundance	1
Lead	decreases expression	1
Methapyrilene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation, increases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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