ATXN7L2

Summary

ATXN7L2 (ataxin 7 like 2, HGNC:28713) is a protein-coding gene on chromosome 1p13.3, encoding Ataxin-7-like protein 2 (Q5T6C5).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 121 total
• MANE Select transcript: NM_001350175

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28713
Approved symbol	ATXN7L2
Name	ataxin 7 like 2
Location	1p13.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC46534, FLJ00381
Ensembl gene	ENSG00000162650
Ensembl biotype	protein_coding
Entrez	127002

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 protein_coding, 4 nonsense_mediated_decay, 2 retained_intron

ENST00000369869, ENST00000369870, ENST00000459635, ENST00000463678, ENST00000497545, ENST00000604728, ENST00000683729, ENST00000684449, ENST00000684472, ENST00000923532, ENST00000923533

RefSeq mRNA: 4 — MANE Select: NM_001350175 NM_001350174, NM_001350175, NM_001350177, NM_153340

CCDS: CCDS30794, CCDS91018, CCDS91019

Canonical transcript exons

ENST00000683729 — 11 exons

Exon	Start	End
ENSE00003494348	109486057	109486122
ENSE00003502085	109488847	109489100
ENSE00003516352	109489930	109490128
ENSE00003529459	109490271	109490392
ENSE00003536066	109488383	109488465
ENSE00003571301	109490922	109491717
ENSE00003574030	109492586	109492734
ENSE00003602658	109486506	109486610
ENSE00003677681	109487007	109487217
ENSE00003920810	109487518	109487804
ENSE00003920844	109483905	109484080

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 88.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.9455 / max 71.5980, expressed in 1660 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4416	6.9455	1660

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	88.83	gold quality
gastrocnemius	UBERON:0001388	88.73	gold quality
muscle of leg	UBERON:0001383	87.76	gold quality
cerebellar hemisphere	UBERON:0002245	87.52	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.40	gold quality
cerebellar cortex	UBERON:0002129	87.27	gold quality
right testis	UBERON:0004534	85.34	gold quality
left testis	UBERON:0004533	84.58	gold quality
cerebellum	UBERON:0002037	84.06	gold quality
right adrenal gland	UBERON:0001233	83.91	gold quality
right frontal lobe	UBERON:0002810	83.76	gold quality
right adrenal gland cortex	UBERON:0035827	83.31	gold quality
right lobe of thyroid gland	UBERON:0001119	82.06	gold quality
left lobe of thyroid gland	UBERON:0001120	81.81	gold quality
left adrenal gland cortex	UBERON:0035825	81.69	gold quality
left adrenal gland	UBERON:0001234	81.64	gold quality
adenohypophysis	UBERON:0002196	81.58	gold quality
metanephros cortex	UBERON:0010533	81.39	gold quality
apex of heart	UBERON:0002098	81.12	gold quality
anterior cingulate cortex	UBERON:0009835	81.07	gold quality
testis	UBERON:0000473	80.89	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.76	gold quality
granulocyte	CL:0000094	80.66	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.58	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.37	gold quality
pituitary gland	UBERON:0000007	79.99	gold quality
ganglionic eminence	UBERON:0004023	79.85	gold quality
thyroid gland	UBERON:0002046	79.77	gold quality
right lobe of liver	UBERON:0001114	79.17	gold quality
adrenal cortex	UBERON:0001235	79.14	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting ATXN7L2, 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-5692A	100.00	74.40	6850
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-4524A-5P	99.57	71.73	1193
HSA-MIR-4524B-5P	99.57	71.68	1195
HSA-MIR-7159-3P	99.51	70.17	1920
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-302A-5P	99.39	68.21	1913
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-6754-5P	98.60	65.54	1627

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	atxn7l2a	ENSDARG00000055300
danio_rerio	atxn7l2b	ENSDARG00000056268
mus_musculus	Atxn7l2	ENSMUSG00000048997
rattus_norvegicus	Atxn7l2	ENSRNOG00000028749

Paralogs (4): ATXN7L3 (ENSG00000087152), ATXN7L1 (ENSG00000146776), ATXN7 (ENSG00000163635), ATXN7L3B (ENSG00000253719)

Protein

Protein identifiers

Ataxin-7-like protein 2 — Q5T6C5 (reviewed: Q5T6C5)

All UniProt accessions (7): A0A804HI28, A0A804HIT1, A0A804HIX1, A0A804HJY2, Q5T6C5, A0A804HKL0, S4R3G5

RefSeq proteins (4): NP_001337103, NP_001337104, NP_001337106, NP_699171 (=MANE)

Domains & families (InterPro)

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

Pfam: PF08313

UniProt features (12 total): region of interest 4, compositionally biased region 4, chain 1, domain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T6C5-F1	54.27	0.05

Functional residue map

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

Post-translational modifications (1): 575

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 123 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, AHRARNT_01, RNGTGGGC_UNKNOWN, AP1_01, GCANCTGNY_MYOD_Q6, ATACCTC_MIR202, MAZ_Q6, USF_C, CAGCTG_AP4_Q5, E2F_Q3, TGCTGAY_UNKNOWN, GATA1_01, HFH8_01, HNF4_DR1_Q3, TGANTCA_AP1_C

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1187 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATXN7L2	ENY2	Q9NPA8	884
ATXN7L2	ATXN7L3	Q14CW9	861
ATXN7L2	TAF9	Q16594	806
ATXN7L2	KAT2B	Q92831	804
ATXN7L2	SORBS1	Q9BX66	793
ATXN7L2	CRX	O43186	791
ATXN7L2	AGXT	P21549	764
ATXN7L2	HTT	P42858	713
ATXN7L2	KAT2A	Q92830	711
ATXN7L2	USP22	Q9UPT9	662
ATXN7L2	ATXN3L	Q9H3M9	652
ATXN7L2	ATXN3	P54252	650
ATXN7L2	ATXN1	P54253	599
ATXN7L2	ATN1	P54259	576
ATXN7L2	NR2E3	Q9Y5X4	563

IntAct

23 interactions, top by confidence:

A	B	Type	Score
TAF12	TAF4	psi-mi:“MI:0914”(association)	0.760
TRRAP	ATXN7	psi-mi:“MI:0914”(association)	0.740
ATXN7L3	USP27X	psi-mi:“MI:0914”(association)	0.640
TSFM	CST4	psi-mi:“MI:0914”(association)	0.530
TSFM	MTIF2	psi-mi:“MI:0914”(association)	0.530
ATXN7L2	PHB2	psi-mi:“MI:0915”(physical association)	0.400
ATXN7L3	USP27X	psi-mi:“MI:0914”(association)	0.350
USP22	CNOT1	psi-mi:“MI:0914”(association)	0.350
SGF29	USP27X	psi-mi:“MI:0914”(association)	0.350
ENY2	EIF3CL	psi-mi:“MI:0914”(association)	0.350
SF3B3	ATXN7	psi-mi:“MI:0914”(association)	0.350
SF3B5	SUPT3H	psi-mi:“MI:0914”(association)	0.350
KLF6	SEC16A	psi-mi:“MI:2364”(proximity)	0.270
MYC	SETD1A	psi-mi:“MI:2364”(proximity)	0.270
ATXN7L2	CBX3	psi-mi:“MI:0915”(physical association)	0.000
ATXN7L2	LAMB1	psi-mi:“MI:0915”(physical association)	0.000
ATXN7L2	PPP2R3A	psi-mi:“MI:0915”(physical association)	0.000
ATXN7L2	MDFI	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (76): ATXN7L2 (Affinity Capture-RNA), ATXN7L2 (Affinity Capture-MS), ATXN7L2 (Affinity Capture-MS), ATXN7L2 (Affinity Capture-MS), ATXN7L2 (Affinity Capture-MS), ATXN7L2 (Affinity Capture-MS), ATXN7L2 (Two-hybrid), ATXN7L2 (Two-hybrid), ATXN7L2 (Two-hybrid), ATXN7L2 (Two-hybrid), ATXN7L2 (Two-hybrid), ATXN7L2 (Two-hybrid), ATXN7L2 (Two-hybrid), ATXN7L2 (Two-hybrid), ATXN7L2 (Two-hybrid)

ESM2 similar proteins: A0JNJ4, A4IHR5, A6H7J1, A7UKY7, D4AE48, E9Q9M8, O15209, O35615, O75081, O95785, P03966, P04198, P39881, P49796, P52746, Q01101, Q1LY51, Q29RS4, Q32KV8, Q4KLY2, Q505G8, Q5T6C5, Q5TJE2, Q61976, Q62511, Q63379, Q63ZV0, Q6AY75, Q6NUJ5, Q6NV74, Q6P0F9, Q7T3H2, Q8BG80, Q8CDC7, Q8CE64, Q8IX07, Q8N554, Q8R4U1, Q96C00, Q96JP5

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 26 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	31.7×	8e-09
Chromatin organization	6	24.5×	7e-06
Chromatin modifying enzymes	6	21.7×	9e-06

GO biological processes:

GO term	Partners	Fold	FDR
regulation of DNA repair	11	116.9×	8e-19
regulation of RNA splicing	10	84.2×	1e-15

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	102
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2185 predictions. Top by Δscore:

Variant	Effect	Δscore
1:109484076:TGACG:T	donor_gain	1.0000
1:109484077:GACG:G	donor_gain	1.0000
1:109484077:GACGG:G	donor_gain	1.0000
1:109484078:ACG:A	donor_gain	1.0000
1:109484078:ACGGT:A	donor_loss	1.0000
1:109484079:CG:C	donor_gain	1.0000
1:109484079:CGGT:C	donor_loss	1.0000
1:109484080:GG:G	donor_gain	1.0000
1:109484081:G:GG	donor_gain	1.0000
1:109486504:A:AG	acceptor_gain	1.0000
1:109486505:G:GG	acceptor_gain	1.0000
1:109486505:GAC:G	acceptor_gain	1.0000
1:109486505:GACAT:G	acceptor_gain	1.0000
1:109486600:G:GT	donor_gain	1.0000
1:109486608:GCG:G	donor_gain	1.0000
1:109486617:G:T	donor_gain	1.0000
1:109486998:T:A	acceptor_gain	1.0000
1:109487516:A:AG	acceptor_gain	1.0000
1:109487517:G:GG	acceptor_gain	1.0000
1:109487800:GGCTC:G	donor_gain	1.0000
1:109487801:GCTC:G	donor_gain	1.0000
1:109487801:GCTCG:G	donor_gain	1.0000
1:109487805:G:GG	donor_gain	1.0000
1:109489098:CAGG:C	donor_loss	1.0000
1:109489102:T:G	donor_loss	1.0000
1:109490268:TAGTT:T	acceptor_loss	1.0000
1:109490269:A:AG	acceptor_gain	1.0000
1:109490269:AGTTC:A	acceptor_loss	1.0000
1:109490270:G:GG	acceptor_gain	1.0000
1:109490270:GT:G	acceptor_gain	1.0000

AlphaMissense

4891 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:109484038:T:A	W29R	1.000
1:109484038:T:C	W29R	1.000
1:109484040:G:C	W29C	1.000
1:109484040:G:T	W29C	1.000
1:109486111:T:A	L61H	1.000
1:109486111:T:C	L61P	1.000
1:109486517:T:C	F69L	1.000
1:109486518:T:C	F69S	1.000
1:109486519:C:A	F69L	1.000
1:109486519:C:G	F69L	1.000
1:109486520:G:A	G70R	1.000
1:109486520:G:C	G70R	1.000
1:109486520:G:T	G70W	1.000
1:109486521:G:A	G70E	1.000
1:109486521:G:T	G70V	1.000
1:109486551:T:C	L80S	1.000
1:109486551:T:G	L80W	1.000
1:109486554:T:A	V81D	1.000
1:109486559:T:A	C83S	1.000
1:109486559:T:C	C83R	1.000
1:109486560:G:A	C83Y	1.000
1:109486560:G:C	C83S	1.000
1:109486560:G:T	C83F	1.000
1:109486561:T:G	C83W	1.000
1:109486568:T:A	C86S	1.000
1:109486568:T:C	C86R	1.000
1:109486569:G:A	C86Y	1.000
1:109486569:G:C	C86S	1.000
1:109486569:G:T	C86F	1.000
1:109486570:C:G	C86W	1.000

dbSNP variants (sampled 300 via entrez): RS1000033955 (1:109484232 C>G,T), RS1000233611 (1:109487560 C>T), RS1000721964 (1:109492488 A>G,T), RS1000753328 (1:109492151 T>C), RS1000987062 (1:109492364 G>C), RS1001397814 (1:109486402 G>A,T), RS1002000211 (1:109482690 A>G), RS1002053971 (1:109482208 T>C), RS1002627147 (1:109489154 A>G), RS1002718305 (1:109485450 C>T), RS1003474910 (1:109483367 C>A,G), RS1003514979 (1:109490214 A>C), RS1003615240 (1:109490513 C>G), RS1003673068 (1:109484338 G>C), RS1004056877 (1:109490571 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

3 associations (top):

Study	Trait	p-value
GCST000578_1	Major depressive disorder	6.000000e-06
GCST000649_1	Chronic kidney disease	1.000000e-07
GCST005316_309	Intelligence (MTAG)	3.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	2
Valproic Acid	increases methylation, affects expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
FR900359	increases phosphorylation	1
trichostatin A	affects expression	1
benzo(e)pyrene	increases methylation	1
cylindrospermopsin	increases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Atrazine	increases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Methapyrilene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Okadaic Acid	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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