WDR31

Summary

WDR31 (WD repeat domain 31, HGNC:21421) is a protein-coding gene on chromosome 9q32, encoding WD repeat-containing protein 31 (Q8NA23).

This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene but the biological validity of some variants has not been determined.

Source: NCBI Gene 114987 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 57 total — 1 likely-pathogenic
• MANE Select transcript: NM_001012361

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21421
Approved symbol	WDR31
Name	WD repeat domain 31
Location	9q32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35921
Ensembl gene	ENSG00000148225
Ensembl biotype	protein_coding
OMIM	620951
Entrez	114987

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 23 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000341761, ENST00000374193, ENST00000461942, ENST00000465205, ENST00000465979, ENST00000865155, ENST00000865156, ENST00000865157, ENST00000865158, ENST00000865159, ENST00000865160, ENST00000865161, ENST00000865162, ENST00000944262, ENST00000944263, ENST00000944264, ENST00000944265, ENST00000944266, ENST00000944267, ENST00000944268, ENST00000944269, ENST00000944270, ENST00000944271, ENST00000944272, ENST00000944273

RefSeq mRNA: 3 — MANE Select: NM_001012361 NM_001006615, NM_001012361, NM_145241

CCDS: CCDS35110, CCDS6792

Canonical transcript exons

ENST00000374193 — 11 exons

Exon	Start	End
ENSE00001091091	113336288	113336440
ENSE00001838862	113340217	113340275
ENSE00003415780	113313222	113316909
ENSE00003510339	113321511	113321578
ENSE00003542239	113320357	113320498
ENSE00003650114	113330984	113331116
ENSE00003663509	113322811	113322911
ENSE00003689702	113328881	113328955
ENSE00003694650	113318475	113318637
ENSE00003729783	113323011	113323155
ENSE00003752182	113331907	113332050

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 83.72.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6774 / max 16.1639, expressed in 444 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
102095	0.5500	339
102096	0.1274	37

Top tissues by expression

247 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	83.72	gold quality
bronchial epithelial cell	CL:0002328	76.49	gold quality
bronchus	UBERON:0002185	74.88	gold quality
heart left ventricle	UBERON:0002084	74.32	gold quality
islet of Langerhans	UBERON:0000006	74.17	gold quality
cardiac ventricle	UBERON:0002082	73.62	gold quality
right adrenal gland	UBERON:0001233	73.32	gold quality
stromal cell of endometrium	CL:0002255	73.05	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	73.04	gold quality
right adrenal gland cortex	UBERON:0035827	72.88	gold quality
left adrenal gland	UBERON:0001234	72.10	gold quality
left adrenal gland cortex	UBERON:0035825	71.47	gold quality
apex of heart	UBERON:0002098	71.33	gold quality
adrenal gland	UBERON:0002369	70.43	gold quality
heart	UBERON:0000948	69.95	gold quality
ventricular zone	UBERON:0003053	69.95	gold quality
right uterine tube	UBERON:0001302	69.80	gold quality
oviduct epithelium	UBERON:0004804	69.79	gold quality
cortical plate	UBERON:0005343	69.75	gold quality
adrenal cortex	UBERON:0001235	69.57	gold quality
prefrontal cortex	UBERON:0000451	68.99	gold quality
upper arm skin	UBERON:0004263	68.93	gold quality
right atrium auricular region	UBERON:0006631	68.33	gold quality
colonic epithelium	UBERON:0000397	68.25	silver quality
smooth muscle tissue	UBERON:0001135	67.86	gold quality
cardiac atrium	UBERON:0002081	67.70	gold quality
pancreas	UBERON:0001264	67.17	gold quality
cardiac muscle of right atrium	UBERON:0003379	66.82	gold quality
right testis	UBERON:0004534	66.62	gold quality
fallopian tube	UBERON:0003889	66.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.19
E-ENAD-27	no	3.91

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting WDR31, 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-12118	100.00	65.88	1270
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-4261	99.59	70.30	3415

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	wdr31	ENSDARG00000073808
mus_musculus	Wdr31	ENSMUSG00000028391
rattus_norvegicus	Wdr31	ENSRNOG00000014869
caenorhabditis_elegans		WBGENE00020231

Protein

Protein identifiers

WD repeat-containing protein 31 — Q8NA23 (reviewed: Q8NA23)

All UniProt accessions (3): Q8NA23, C9JWF1, F8WDK4

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NA23-1	1	yes
Q8NA23-2	2

RefSeq proteins (3): NP_001006616, NP_001012361, NP_660284 (=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
IPR040066	WDR31	Family

Pfam: PF00400

UniProt features (10 total): repeat 7, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NA23-F1	85.43	0.78

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 74 (showing top): MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, YOSHIMURA_MAPK8_TARGETS_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MEISSNER_NPC_HCP_WITH_H3K4ME2, FIGUEROA_AML_METHYLATION_CLUSTER_4_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, LIM_MAMMARY_STEM_CELL_DN, DURAND_STROMA_NS_UP, CRX_DN.V1_UP, NRL_DN.V1_DN, ALKBH3_TARGET_GENES, DIDO1_TARGET_GENES, HDAC4_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

3252 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR31	SMKR1	H3BMG3	524
WDR31	PGAP4	Q9BRR3	461
WDR31	NPIPB9	F8W1W9	447
WDR31	TMEM273	Q5T292	445
WDR31	RGS9BP	Q6ZS82	435
WDR31	ANKRD66	B4E2M5	418
WDR31	HEATR5B	Q9P2D3	417
WDR31	STX2	P32856	415
WDR31	ACP7	Q6ZNF0	406
WDR31	SERTAD4	Q9NUC0	373
WDR31	TTC23	Q5W5X9	372
WDR31	WDR70	Q9NW82	371
WDR31	FAM169A	Q9Y6X4	363
WDR31	DYNC2I2	Q96EX3	350
WDR31	EIF6	P56537	349

IntAct

3 interactions, top by confidence:

A	B	Type	Score
LAMP2	WDR31	psi-mi:“MI:0915”(physical association)	0.400
WDR31	NUDC	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (1): WDR31 (Synthetic Lethality)

ESM2 similar proteins: A0A1L8HX76, A0JP70, A4IG72, A7E3S5, A7Z052, D3ZW91, E9PY46, P57081, Q05B17, Q0P5H9, Q15061, Q32P44, Q3SZD4, Q3U821, Q499N3, Q4VBE8, Q5BK48, Q5F3K4, Q5RB07, Q5RBH8, Q5RD06, Q5XFW6, Q68EI0, Q6DFC6, Q6KAU8, Q6PFM9, Q6PGF3, Q6ZQL4, Q7ZVF0, Q7ZVR1, Q7ZY78, Q8BH57, Q8C5V5, Q8IWA0, Q8N0Z6, Q8NA23, Q8NAA4, Q8VC03, Q969R8, Q96KV7

Diamond homologs: A6H603, O14011, O22785, P25635, P32523, Q08E38, Q10051, Q55AR8, Q5ZMA2, Q7KWK5, Q86H45, Q8NA23, Q94BR4, Q99KP6, Q9AV81, Q9JMJ4, Q9UMS4, Q9HAD4, Q9JHB4, Q3UDP0, Q21215

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	42
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1527542	GRCh37/hg19 9q31.2-32(chr9:109265628-117650999)	Likely pathogenic

SpliceAI

1828 predictions. Top by Δscore:

Variant	Effect	Δscore
9:113320335:TGG:T	donor_gain	1.0000
9:113320499:C:CC	acceptor_gain	1.0000
9:113336441:C:CC	acceptor_gain	1.0000
9:113339081:C:A	donor_gain	1.0000
9:113320495:TAAT:T	acceptor_gain	0.9900
9:113320496:AATC:A	acceptor_loss	0.9900
9:113320497:AT:A	acceptor_gain	0.9900
9:113320498:TCTG:T	acceptor_loss	0.9900
9:113320499:CTGAA:C	acceptor_loss	0.9900
9:113322816:T:A	donor_gain	0.9900
9:113336286:ACCC:A	donor_gain	0.9900
9:113336287:CCCC:C	donor_gain	0.9900
9:113336439:CA:C	acceptor_gain	0.9900
9:113318638:C:CC	acceptor_gain	0.9800
9:113323008:TAC:T	donor_loss	0.9800
9:113323009:AC:A	donor_loss	0.9800
9:113323010:C:A	donor_loss	0.9800
9:113328952:CTGT:C	acceptor_gain	0.9800
9:113330988:T:C	donor_gain	0.9800
9:113336279:ATTAC:A	donor_loss	0.9800
9:113336280:TTAC:T	donor_loss	0.9800
9:113336281:TACT:T	donor_loss	0.9800
9:113336282:ACTT:A	donor_loss	0.9800
9:113336283:CTTAC:C	donor_loss	0.9800
9:113336284:T:TG	donor_loss	0.9800
9:113336285:TACCC:T	donor_loss	0.9800
9:113336286:A:G	donor_loss	0.9800
9:113336286:AC:A	donor_gain	0.9800
9:113336287:CC:C	donor_gain	0.9800
9:113336436:TTGCA:T	acceptor_gain	0.9800

AlphaMissense

2405 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:113323120:A:C	S120R	0.998
9:113323120:A:T	S120R	0.998
9:113323122:T:G	S120R	0.998
9:113323092:A:G	W130R	0.991
9:113323092:A:T	W130R	0.991
9:113318493:A:G	W309R	0.990
9:113318493:A:T	W309R	0.990
9:113318634:A:G	W262R	0.990
9:113318634:A:T	W262R	0.990
9:113331003:A:T	V77D	0.988
9:113323034:A:T	V149D	0.986
9:113323090:C:A	W130C	0.985
9:113323090:C:G	W130C	0.985
9:113318525:G:T	A298D	0.984
9:113320494:A:G	W215R	0.984
9:113320494:A:T	W215R	0.984
9:113322888:A:G	S165P	0.984
9:113322890:C:T	G164D	0.984
9:113323118:G:T	A121D	0.981
9:113331001:A:G	S78P	0.979
9:113316824:A:C	S343R	0.977
9:113316824:A:T	S343R	0.977
9:113316826:T:G	S343R	0.977
9:113318598:A:C	Y274D	0.977
9:113318632:C:A	W262C	0.975
9:113318632:C:G	W262C	0.975
9:113322882:C:G	D167H	0.974
9:113323116:A:G	S122P	0.974
9:113330997:C:T	G79E	0.974
9:113318491:C:A	W309C	0.973

dbSNP variants (sampled 300 via entrez): RS1000177032 (9:113325262 G>A), RS1000228024 (9:113324844 G>A), RS1000332176 (9:113316393 C>T), RS1000535358 (9:113339472 T>C), RS1000662775 (9:113335906 G>T), RS1000969956 (9:113313744 C>A,T), RS1000992456 (9:113339208 A>T), RS1001160945 (9:113323219 A>G), RS1001676202 (9:113316664 C>T), RS1001793419 (9:113329157 G>T), RS1001855235 (9:113323811 A>C), RS1001909245 (9:113323541 C>G,T), RS1002134520 (9:113316878 T>C), RS1002207766 (9:113337835 T>C,G), RS1002323294 (9:113329042 C>T)

Disease associations

OMIM: gene MIM:620951 | 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
GCST90002407_122	White blood cell count	3.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
jinfukang	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Folic Acid	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression	1
Gold Compounds	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1
Particulate Matter	increases expression, increases abundance	1

Clinical trials (associated diseases)

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