WDR97

Summary

WDR97 (WD repeat domain 97, HGNC:26959) is a protein-coding gene on chromosome 8q24.3, encoding WD repeat-containing protein 97 (A6NE52).

The function and protein-coding potential of this gene is unknown. The exon combination is based on AB058778.1 for which two possible open reading frames can be predicted (with start codons at nucleotide 26 or 2614). The position of the first ORF stop codon is consistent with a prediction of nonsense-mediated decay. Given the observation of the first ORF and its length, a predicted translation of the second ORF is inconsistent with the translation leaky scanning theory. Therefore, this gene is represented as a non-protein-coding transcript.

Source: NCBI Gene 340390 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_001316309

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26959
Approved symbol	WDR97
Name	WD repeat domain 97
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000179698
Ensembl biotype	protein_coding
Entrez	340390

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 retained_intron, 1 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000323662, ENST00000525150, ENST00000528691, ENST00000529209, ENST00000533108, ENST00000534167

RefSeq mRNA: 1 — MANE Select: NM_001316309 NM_001316309

CCDS: CCDS83334

Canonical transcript exons

ENST00000323662 — 24 exons

Exon	Start	End
ENSE00001265251	144109335	144110034
ENSE00001265258	144109049	144109170
ENSE00001300264	144108059	144108195
ENSE00001317692	144108316	144108944
ENSE00001650878	144111426	144111486
ENSE00001745489	144111101	144111222
ENSE00003490689	144110114	144110256
ENSE00003506400	144110649	144110739
ENSE00003510108	144110864	144110996
ENSE00003536378	144115341	144115858
ENSE00003556833	144116091	144118328
ENSE00003562923	144111887	144112144
ENSE00003573840	144112224	144112349
ENSE00003589178	144113977	144114162
ENSE00003595310	144113440	144113517
ENSE00003600221	144114749	144114911
ENSE00003621197	144114554	144114675
ENSE00003635065	144111632	144111781
ENSE00003636278	144110341	144110577
ENSE00003669645	144112447	144112530
ENSE00003675863	144115943	144116013
ENSE00003685134	144113657	144113881
ENSE00003692079	144114278	144114475
ENSE00003895398	144107739	144107862

Expression profiles

Bgee: expression breadth ubiquitous, 151 present calls, max score 84.56.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5576 / max 16.6289, expressed in 236 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
91485	0.2781	168
91484	0.2371	127
91483	0.0424	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	84.56	gold quality
right testis	UBERON:0004534	84.17	gold quality
testis	UBERON:0000473	80.12	gold quality
right hemisphere of cerebellum	UBERON:0014890	79.89	gold quality
cerebellar hemisphere	UBERON:0002245	78.39	gold quality
cerebellar cortex	UBERON:0002129	78.08	gold quality
cerebellum	UBERON:0002037	75.42	gold quality
right frontal lobe	UBERON:0002810	73.14	gold quality
adenohypophysis	UBERON:0002196	71.66	gold quality
cortical plate	UBERON:0005343	71.28	gold quality
pituitary gland	UBERON:0000007	70.67	gold quality
right lobe of liver	UBERON:0001114	70.60	gold quality
sural nerve	UBERON:0015488	70.30	gold quality
right uterine tube	UBERON:0001302	69.58	gold quality
granulocyte	CL:0000094	69.36	gold quality
left lobe of thyroid gland	UBERON:0001120	69.29	gold quality
right lobe of thyroid gland	UBERON:0001119	69.23	gold quality
thyroid gland	UBERON:0002046	67.89	gold quality
nucleus accumbens	UBERON:0001882	67.65	gold quality
Brodmann (1909) area 9	UBERON:0013540	67.35	gold quality
stromal cell of endometrium	CL:0002255	67.00	gold quality
hypothalamus	UBERON:0001898	66.78	gold quality
anterior cingulate cortex	UBERON:0009835	66.28	gold quality
metanephros cortex	UBERON:0010533	65.64	gold quality
mucosa of transverse colon	UBERON:0004991	65.14	gold quality
putamen	UBERON:0001874	65.00	gold quality
apex of heart	UBERON:0002098	64.96	gold quality
amygdala	UBERON:0001876	64.94	gold quality
caudate nucleus	UBERON:0001873	64.74	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	64.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.19

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

WD repeat-containing protein 97 — A6NE52 (reviewed: A6NE52)

All UniProt accessions (2): A6NE52, E9PKB8

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
A6NE52-1	1	yes
A6NE52-2	2

RefSeq proteins (1): NP_001303238* (*=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
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily

Pfam: PF00400

UniProt features (17 total): repeat 6, sequence variant 3, splice variant 2, region of interest 2, chain 1, compositionally biased region 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NE52-F1	62.16	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): CTCAAGA_MIR526B, MARTENS_TRETINOIN_RESPONSE_UP, chr8q24, SNAPC4_TARGET_GENES, BLANCO_MELO_HUMAN_PARAINFLUENZA_VIRUS_3_INFECTION_A594_CELLS_DN, BLANCO_MELO_RESPIRATORY_SYNCYTIAL_VIRUS_INFECTION_A594_CELLS_DN, MANNO_MIDBRAIN_NEUROTYPES_HGABA, DESCARTES_MAIN_FETAL_CCL19_CCL21_POSITIVE_CELLS, DESCARTES_FETAL_PANCREAS_CCL19_CCL21_POSITIVE_CELLS, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_2H_ACT_CD4_TCELL_UP, GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_UP, GSE41867_NAIVE_VS_DAY15_LCMV_CONE13_EFFECTOR_CD8_TCELL_UP, GSE41867_NAIVE_VS_DAY30_LCMV_CLONE13_EXHAUSTED_CD8_TCELL_UP, GSE41867_DAY6_VS_DAY15_LCMV_CLONE13_EFFECTOR_CD8_TCELL_UP, GSE41867_DAY8_VS_DAY15_LCMV_ARMSTRONG_EFFECTOR_CD8_TCELL_DN

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

1451 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR97	ZNF837	Q96EG3	549
WDR97	ANKRD62	A6NC57	513
WDR97	ZNF707	Q96C28	483
WDR97	LRRC24	Q50LG9	479
WDR97	GPAA1	O43292	475
WDR97	RWDD4	Q6NW29	475
WDR97	LRRC14	Q15048	470
WDR97	GLI4	P10075	453
WDR97	MROH1	Q8NDA8	434
WDR97	LCN6	P62502	419
WDR97	ADCK5	Q3MIX3	413
WDR97	FBXL6	Q8N531	409
WDR97	HSDL2	Q6YN16	408
WDR97	EXOSC4	Q9NPD3	403
WDR97	SHROOM1	Q2M3G4	401

IntAct

2 interactions, top by confidence:

A	B	Type	Score
WDR97	FBXW7	psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: A0JMF1, A2CI97, A3KNA7, A6NE52, B2GV47, E7FAW3, P60330, Q06ZW3, Q0VDN7, Q12769, Q1M161, Q2NKJ3, Q2YDQ5, Q3SYW0, Q3T1I9, Q3U6Q4, Q4FZR5, Q5EE38, Q5PNP6, Q5RDX3, Q5SUQ9, Q5TYP4, Q5ZIB8, Q6AYM1, Q6DG91, Q6IRN0, Q6NSI4, Q6NYX6, Q6P4K6, Q6PH58, Q6ZNJ1, Q6ZPG2, Q6ZQA0, Q7T006, Q7ZVM9, Q80TE0, Q80VA5, Q8BJW5, Q8BMG1, Q8C779

Diamond homologs: A1CF18, A4R3M4, A6NE52, B6QC56, B8M0Q1, B8N9H4, C0NRC6, C4JPW9, C5FWH1, C5PFX0, C6HTE8, Q2HBX6, Q2UGU1, Q54RP0, Q5FVB6, A1CH75, A1CXL0, A2QI22, A3LQ86, A4R2Q6, A5DL92, A5DST9, A6R3K5, A6S0T8, A6ZPA9, A7ECP3, A7TMF9, A8PD13, B0DWM8, B0Y5V6, B2B5V0, B2VZH2, B3RQN1, C4Y5P7, C4YN69, G0SFB5, O94289, P38262, P41318, Q0CLJ4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3641 predictions. Top by Δscore:

Variant	Effect	Δscore
8:144108472:G:GT	donor_gain	1.0000
8:144111778:GCTG:G	donor_gain	1.0000
8:144112348:GG:G	donor_gain	1.0000
8:144112349:GG:G	donor_gain	1.0000
8:144116011:GGG:G	donor_gain	1.0000
8:144116012:GGG:G	donor_gain	1.0000
8:144107858:GAATG:G	donor_gain	0.9900
8:144110020:G:GT	donor_gain	0.9900
8:144110108:TCGCA:T	acceptor_loss	0.9900
8:144110109:CGCA:C	acceptor_loss	0.9900
8:144110110:GCAG:G	acceptor_loss	0.9900
8:144110111:CA:C	acceptor_loss	0.9900
8:144110112:A:C	acceptor_loss	0.9900
8:144110113:G:GC	acceptor_loss	0.9900
8:144110553:G:GT	donor_gain	0.9900
8:144111252:G:GT	donor_gain	0.9900
8:144111484:G:GT	donor_gain	0.9900
8:144111734:G:GT	donor_gain	0.9900
8:144111779:CTGG:C	donor_loss	0.9900
8:144111780:TGG:T	donor_loss	0.9900
8:144111782:G:GG	donor_gain	0.9900
8:144111782:GT:G	donor_loss	0.9900
8:144112216:T:G	acceptor_gain	0.9900
8:144112216:T:TA	acceptor_gain	0.9900
8:144112222:A:AG	acceptor_gain	0.9900
8:144112223:G:GG	acceptor_gain	0.9900
8:144112345:GCAGG:G	donor_gain	0.9900
8:144112347:AGG:A	donor_loss	0.9900
8:144112348:GGG:G	donor_loss	0.9900
8:144112349:GGTG:G	donor_loss	0.9900

AlphaMissense

10363 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:144109412:T:A	W360R	0.995
8:144109412:T:C	W360R	0.995
8:144110690:A:C	S708R	0.995
8:144110692:C:A	S708R	0.995
8:144110692:C:G	S708R	0.995
8:144109414:G:C	W360C	0.994
8:144109414:G:T	W360C	0.994
8:144109125:T:A	W319R	0.993
8:144109125:T:C	W319R	0.993
8:144109407:G:C	R358P	0.993
8:144110364:T:A	W623R	0.993
8:144110364:T:C	W623R	0.993
8:144110714:T:A	W716R	0.993
8:144110714:T:C	W716R	0.993
8:144109127:G:C	W319C	0.992
8:144109127:G:T	W319C	0.992
8:144110682:C:A	A705D	0.991
8:144110709:G:C	R714P	0.988
8:144110901:T:C	F737L	0.988
8:144110903:C:A	F737L	0.988
8:144110903:C:G	F737L	0.988
8:144109121:G:C	K317N	0.987
8:144109121:G:T	K317N	0.987
8:144110706:T:A	V713D	0.987
8:144108739:T:C	F225L	0.986
8:144108741:C:A	F225L	0.986
8:144108741:C:G	F225L	0.986
8:144110366:G:C	W623C	0.986
8:144110366:G:T	W623C	0.986
8:144110716:G:C	W716C	0.986

dbSNP variants (sampled 300 via entrez): RS1000007447 (8:144112587 C>G,T), RS1000293818 (8:144116981 C>A,G,T), RS1000481167 (8:144107419 C>G,T), RS1000506680 (8:144116307 C>G,T), RS1000665770 (8:144117304 G>C), RS1000776481 (8:144112652 C>A), RS1001252462 (8:144110171 G>A), RS1001724970 (8:144109891 C>G,T), RS1002327744 (8:144108472 G>A), RS1002349185 (8:144116076 TCCGC>T), RS1002374389 (8:144118545 C>T), RS1002414907 (8:144113835 G>A), RS1002999091 (8:144111054 G>A), RS1003056186 (8:144116176 G>A), RS1003273785 (8:144110843 C>T)

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

3 associations (top):

Study	Trait	p-value
GCST009798_65	Asthma	1.000000e-08
GCST012353_35	Serum metabolite concentrations in chronic kidney disease	2.000000e-22
GCST90020029_58	Waist circumference adjusted for body mass index	1.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects expression, increases abundance, increases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
tri-o-cresyl phosphate	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Ozone	increases abundance, affects expression	1
Polychlorinated Biphenyls	affects expression	1
Smoke	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1
Okadaic Acid	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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