ATXN7L1

Summary

ATXN7L1 (ataxin 7 like 1, HGNC:22210) is a protein-coding gene on chromosome 7q22.3, encoding Ataxin-7-like protein 1 (Q9ULK2).

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 155 total — 3 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_020725

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22210
Approved symbol	ATXN7L1
Name	ataxin 7 like 1
Location	7q22.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1218, MGC33190
Ensembl gene	ENSG00000146776
Ensembl biotype	protein_coding
Entrez	222255

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 6 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000318724, ENST00000419735, ENST00000464874, ENST00000472195, ENST00000472910, ENST00000474433, ENST00000477775, ENST00000478915, ENST00000481880, ENST00000484475, ENST00000485652

RefSeq mRNA: 5 — MANE Select: NM_020725 NM_001318229, NM_001385596, NM_020725, NM_138495, NM_152749

CCDS: CCDS34727, CCDS47682, CCDS47683

Canonical transcript exons

ENST00000419735 — 12 exons

Exon	Start	End
ENSE00001643471	105788604	105788708
ENSE00001682841	105610529	105610603
ENSE00001708082	105604772	105607890
ENSE00001805291	105613862	105614816
ENSE00002159631	105876378	105876599
ENSE00003487748	105624075	105624267
ENSE00003558717	105875812	105875880
ENSE00003622727	105642838	105643121
ENSE00003658683	105665066	105665288
ENSE00003681009	105638353	105638609
ENSE00003682677	105620200	105620321
ENSE00003684471	105639487	105639569

Expression profiles

Bgee: expression breadth ubiquitous, 232 present calls, max score 86.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.9954 / max 199.0094, expressed in 1730 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85460	6.1688	1640
85447	1.8335	404
85461	0.9182	286
85448	0.8073	223
85449	0.7457	197
85446	0.5421	212
85451	0.4893	114
85453	0.3090	107
85450	0.1170	56
85452	0.0646	40

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	86.29	gold quality
secondary oocyte	CL:0000655	86.03	gold quality
sural nerve	UBERON:0015488	85.86	gold quality
cortical plate	UBERON:0005343	84.70	gold quality
left testis	UBERON:0004533	84.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.64	gold quality
monocyte	CL:0000576	83.39	gold quality
mononuclear cell	CL:0000842	83.09	gold quality
leukocyte	CL:0000738	83.04	gold quality
calcaneal tendon	UBERON:0003701	82.96	gold quality
right testis	UBERON:0004534	82.87	gold quality
testis	UBERON:0000473	82.22	gold quality
small intestine Peyer’s patch	UBERON:0003454	81.92	gold quality
oocyte	CL:0000023	81.74	gold quality
mucosa of transverse colon	UBERON:0004991	81.21	gold quality
colonic epithelium	UBERON:0000397	81.05	gold quality
small intestine	UBERON:0002108	80.50	gold quality
rectum	UBERON:0001052	80.22	gold quality
buccal mucosa cell	CL:0002336	79.99	silver quality
adrenal tissue	UBERON:0018303	79.39	gold quality
granulocyte	CL:0000094	79.07	gold quality
lower esophagus mucosa	UBERON:0035834	78.11	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.62	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.61	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	77.59	gold quality
transverse colon	UBERON:0001157	77.54	gold quality
metanephros cortex	UBERON:0010533	77.27	gold quality
blood	UBERON:0000178	77.13	gold quality
skin of leg	UBERON:0001511	77.03	gold quality
bone marrow cell	CL:0002092	76.95	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting ATXN7L1, 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-371A-3P	99.99	66.77	91
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-1294	98.91	69.26	1030
HSA-MIR-9986	98.91	69.28	1024
HSA-MIR-6889-3P	98.84	67.35	1198
HSA-MIR-6529-3P	98.68	66.76	1020
HSA-MIR-8078	98.32	65.73	361
HSA-MIR-6747-5P	96.17	64.99	743
HSA-MIR-29C-5P	87.36	66.96	29

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	atxn7l1	ENSDARG00000089860
mus_musculus	Atxn7l1	ENSMUSG00000020564
rattus_norvegicus	Atxn7l1	ENSRNOG00000010415

Paralogs (4): ATXN7L3 (ENSG00000087152), ATXN7L2 (ENSG00000162650), ATXN7 (ENSG00000163635), ATXN7L3B (ENSG00000253719)

Protein

Protein identifiers

Ataxin-7-like protein 1 — Q9ULK2 (reviewed: Q9ULK2)

Alternative names: Ataxin-7-like protein 4

All UniProt accessions (5): Q9ULK2, C9IZF2, C9K0V9, F8WDE7, H0Y8A2

UniProt curated annotations — full annotation on UniProt →

Isoforms (3)

UniProt ID	Names	Canonical?
Q9ULK2-1	1	yes
Q9ULK2-2	2
Q9ULK2-3	3

RefSeq proteins (5): NP_001305158, NP_001372525, NP_065776, NP_612504, NP_689962 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013243	SCA7_dom	Domain
IPR052237	Ataxin-7-like_regulator	Family

Pfam: PF08313

UniProt features (22 total): compositionally biased region 11, region of interest 5, splice variant 4, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9ULK2-F1	51.61	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 230 (showing top): RNGTGGGC_UNKNOWN, WANG_CLIM2_TARGETS_UP, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, LUCAS_HNF4A_TARGETS_UP, FOXO4_01, FOXO1_01, CHX10_01, SREBP1_02, FOSTER_TOLERANT_MACROPHAGE_DN, FREAC3_01, TGTGTGA_MIR377, FOXJ2_01, HFH4_01, ZIC1_01, HFH3_01

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

1178 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATXN7L1	ENY2	Q9NPA8	881
ATXN7L1	ATXN7L3	Q14CW9	853
ATXN7L1	TAF9	Q16594	806
ATXN7L1	KAT2B	Q92831	799
ATXN7L1	CRX	O43186	788
ATXN7L1	SORBS1	Q9BX66	788
ATXN7L1	AGXT	P21549	760
ATXN7L1	HTT	P42858	710
ATXN7L1	KAT2A	Q92830	704
ATXN7L1	USP22	Q9UPT9	644
ATXN7L1	ATXN3L	Q9H3M9	640
ATXN7L1	ATXN3	P54252	632
ATXN7L1	ATXN1	P54253	589
ATXN7L1	ATXN2	Q99700	575
ATXN7L1	ATN1	P54259	570

IntAct

34 interactions, top by confidence:

A	B	Type	Score
SGF29	NDC80	psi-mi:“MI:0914”(association)	0.840
ATXN7L1	USP22	psi-mi:“MI:0407”(direct interaction)	0.790
ATXN7L1	USP22	psi-mi:“MI:0915”(physical association)	0.790
TAF12	TAF4	psi-mi:“MI:0914”(association)	0.760
ATXN7L3	USP27X	psi-mi:“MI:0914”(association)	0.640
PHF1	ATXN7L1	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	ATXN7L1	psi-mi:“MI:0915”(physical association)	0.560
KRT31	ATXN7L1	psi-mi:“MI:0915”(physical association)	0.560
ATXN7L1	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.560
ATXN7L1	KRT31	psi-mi:“MI:0915”(physical association)	0.560
ATXN7L1	CS	psi-mi:“MI:0915”(physical association)	0.400
ATXN7L1	MRPS9	psi-mi:“MI:0915”(physical association)	0.400
ATXN7L1	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
ATXN7L1	HMGN2	psi-mi:“MI:0915”(physical association)	0.400
ATXN7L1	ATXN7L1	psi-mi:“MI:0915”(physical association)	0.400
ATXN7L1	ATXN7	psi-mi:“MI:0915”(physical association)	0.400
ZNF862	ATXN7L1	psi-mi:“MI:0915”(physical association)	0.370
ATXN7L1	ELP1	psi-mi:“MI:0914”(association)	0.350
ENY2	EIF3CL	psi-mi:“MI:0914”(association)	0.350
USP22	ARPC2	psi-mi:“MI:0914”(association)	0.350
ATXN7L1	USP27X	psi-mi:“MI:0914”(association)	0.350
ATXN7L1	GABARAP	psi-mi:“MI:0914”(association)	0.350

BioGRID (87): ATXN7L1 (Two-hybrid), ATXN7L1 (Two-hybrid), ATXN7L1 (Two-hybrid), KRTAP10-9 (Two-hybrid), ATXN7L1 (Affinity Capture-MS), ATXN7L1 (Synthetic Growth Defect), ATXN7L1 (Affinity Capture-MS), ATXN7L1 (Affinity Capture-RNA), ATXN7L1 (Two-hybrid), ATXN7L1 (Two-hybrid), VENTX (Two-hybrid), ROR2 (Two-hybrid), ATXN7L1 (Proximity Label-MS), ATXN7L1 (Proximity Label-MS), ATXN7L1 (Proximity Label-MS)

ESM2 similar proteins: A0JME2, A2AUY4, A5GFT6, A5X7A0, A7XYH5, A7XYH9, A7XYI6, A7XYQ1, B3DJM5, D3ZKB9, D4A666, E1B7L7, E7F888, O15014, O15265, Q0P5V2, Q14687, Q2HNT1, Q2HNT2, Q3U3C9, Q56A10, Q5DTH5, Q5EAW9, Q5F489, Q5HZG4, Q5VWG9, Q5ZIE8, Q5ZM88, Q63HK5, Q68FE9, Q69ZK6, Q6ZQ03, Q6ZSZ6, Q6ZU65, Q76L83, Q7SXB5, Q80WC1, Q8BZ32, Q8BZ47, Q8CGV9

Diamond homologs: O15265, O94397, P0DH66, P0DH68, P53165, Q3T136, Q5T6C5, Q8R4I1, Q9CZ05, Q9ULK2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 27 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
HATs acetylate histones	8	30.2×	2e-08
Chromatin organization	5	19.4×	4e-04
Chromatin modifying enzymes	5	17.2×	5e-04

GO biological processes:

GO term	Partners	Fold	FDR
regulation of DNA repair	7	77.3×	5e-10
regulation of RNA splicing	6	52.5×	1e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	1
Uncertain significance	126
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
2424385	NC_000007.13:g.(?104456677)(108155935_?)del	Pathogenic
2685260	GRCh37/hg19 7q22.3-31.1(chr7:104536649-109624996)x1	Pathogenic
3245840	NC_000007.13:g.(?102937907)(108155935_?)del	Pathogenic
805919	GRCh37/hg19 7q22.1-22.3(chr7:103679146-105547471)	Likely pathogenic

SpliceAI

3611 predictions. Top by Δscore:

Variant	Effect	Δscore
7:105620193:CACT:C	donor_loss	1.0000
7:105620194:A:AC	donor_gain	1.0000
7:105620195:C:CC	donor_gain	1.0000
7:105620195:CTTA:C	donor_gain	1.0000
7:105620196:TT:T	donor_loss	1.0000
7:105620198:A:AC	donor_gain	1.0000
7:105620198:ACTT:A	donor_gain	1.0000
7:105620199:C:CA	donor_gain	1.0000
7:105620199:CTT:C	donor_gain	1.0000
7:105620199:CTTC:C	donor_gain	1.0000
7:105620201:T:TA	donor_gain	1.0000
7:105620317:CAAAA:C	acceptor_gain	1.0000
7:105620322:C:CC	acceptor_gain	1.0000
7:105624109:CAGT:C	donor_gain	1.0000
7:105627053:A:AC	donor_gain	1.0000
7:105627054:A:C	donor_gain	1.0000
7:105639566:CTCT:C	acceptor_gain	1.0000
7:105639570:C:CC	acceptor_gain	1.0000
7:105639575:T:TC	acceptor_gain	1.0000
7:105642833:CATA:C	donor_loss	1.0000
7:105642834:ATACC:A	donor_loss	1.0000
7:105642835:TAC:T	donor_loss	1.0000
7:105642836:ACC:A	donor_loss	1.0000
7:105642837:CCTGA:C	donor_loss	1.0000
7:105876373:CTTA:C	donor_loss	1.0000
7:105876375:TAC:T	donor_loss	1.0000
7:105876376:A:AC	donor_gain	1.0000
7:105876376:ACT:A	donor_loss	1.0000
7:105876376:ACTGT:A	donor_gain	1.0000
7:105876377:C:CT	donor_gain	1.0000

AlphaMissense

5589 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:105638535:T:A	K340N	1.000
7:105638535:T:G	K340N	1.000
7:105638537:T:C	K340E	1.000
7:105638540:G:C	H339D	1.000
7:105638548:A:G	L336P	1.000
7:105638548:A:T	L336Q	1.000
7:105638551:A:G	L335P	1.000
7:105638559:A:C	F332L	1.000
7:105638559:A:T	F332L	1.000
7:105638560:A:C	F332C	1.000
7:105638560:A:G	F332S	1.000
7:105638561:A:G	F332L	1.000
7:105638573:G:C	R328G	1.000
7:105638581:A:T	V325D	1.000
7:105638586:C:A	R323S	1.000
7:105638586:C:G	R323S	1.000
7:105638587:C:A	R323M	1.000
7:105638587:C:G	R323T	1.000
7:105638588:T:C	R323G	1.000
7:105638590:C:G	R322P	1.000
7:105638591:G:A	R322W	1.000
7:105638591:G:C	R322G	1.000
7:105638599:A:T	L319Q	1.000
7:105638604:A:C	H317Q	1.000
7:105638604:A:T	H317Q	1.000
7:105638605:T:C	H317R	1.000
7:105638606:G:C	H317D	1.000
7:105638606:G:T	H317N	1.000
7:105639489:T:C	K315E	1.000
7:105639490:G:C	C314W	1.000

dbSNP variants (sampled 300 via entrez): RS1000004182 (7:105651782 C>T), RS1000005540 (7:105653320 T>C), RS1000036951 (7:105652097 A>G), RS1000039621 (7:105646927 CA>C), RS1000046300 (7:105733122 G>A,T), RS1000073708 (7:105852612 G>A), RS1000080589 (7:105779434 G>A), RS1000083625 (7:105866439 T>C), RS1000083974 (7:105816690 T>C), RS1000098903 (7:105846925 AAGTTGATTCGTAGTTGCC>A), RS1000103865 (7:105689544 C>T), RS1000107982 (7:105696219 T>C), RS1000132347 (7:105711764 G>A), RS1000136317 (7:105816989 C>T), RS1000145619 (7:105687730 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

12 associations (top):

Study	Trait	p-value
GCST001658_8	Alzheimer’s disease (late onset)	1.000000e-06
GCST001713_11	Dental caries	6.000000e-07
GCST001762_351	Obesity-related traits	8.000000e-06
GCST001762_720	Obesity-related traits	2.000000e-06
GCST005918_1	Smoking cessation in chronic obstructive pulmonary disease	2.000000e-07
GCST006288_103	Heel bone mineral density	2.000000e-10
GCST006288_651	Heel bone mineral density	1.000000e-21
GCST006288_757	Heel bone mineral density	5.000000e-12
GCST006979_145	Heel bone mineral density	7.000000e-55
GCST006988_30	Blond vs. brown/black hair color	3.000000e-14
GCST90002381_458	Eosinophil count	7.000000e-11
GCST90002382_158	Eosinophil percentage of white cells	1.000000e-11

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0005109	energy expenditure
EFO:0005108	arm span
EFO:0004319	smoking cessation
EFO:0009270	heel bone mineral density
EFO:0003924	hair color
EFO:0004842	eosinophil count
EFO:0007991	eosinophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	5
bisphenol A	affects cotreatment, decreases methylation, increases expression	4
Valproic Acid	affects cotreatment, increases expression, decreases expression, decreases methylation	4
Aflatoxin B1	affects expression, decreases methylation, increases methylation	3
Acetaminophen	decreases expression, increases expression	2
Cisplatin	affects cotreatment, decreases expression	2
Cyclosporine	decreases expression, decreases methylation	2
Cadmium Chloride	decreases expression, increases abundance	2
triphenyl phosphate	affects expression	1
trichostatin A	decreases expression	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
nickel sulfate	increases expression	1
epigallocatechin gallate	increases expression, affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
tebuconazole	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Vorinostat	affects cotreatment, increases expression	1
Cadmium	decreases expression, increases abundance	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Hydralazine	increases expression, affects cotreatment	1
Indomethacin	affects cotreatment, increases expression	1
Chlordecone	affects response to substance	1

Clinical trials (associated diseases)

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