Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	51062
Gene name	Atlastin GTPase 1
Gene symbol	ATL1
Synonyms (NCBI Gene)	AD-FSPATL-1FSP1GBP3HSN1DSPG3SPG3Aatlastin1
Chromosome	14
Chromosome location	14q22.1
Summary	The protein encoded by this gene is a GTPase and a Golgi body transmembrane protein. The encoded protein can form a homotetramer and has been shown to interact with spastin and with mitogen-activated protein kinase kinase kinase kinase 4. This protein may

Show/Hide all (42)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28939094	A>G,T	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant
rs119476046	C>T	Pathogenic, pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs119476047	C>A	Pathogenic	Missense variant, coding sequence variant
rs119476048	A>G	Pathogenic	Missense variant, coding sequence variant
rs119476049	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs119476050	C>T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs119476051	T>G	Pathogenic	Missense variant, coding sequence variant
rs137852657	C>T	Pathogenic	Missense variant, coding sequence variant
rs144792471	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, synonymous variant
rs149340140	C>G,T	Benign, uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, synonymous variant
rs186528086	T>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Intron variant
rs200314808	G>A,C	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs387906941	C>T	Pathogenic	Coding sequence variant, missense variant
rs397514712	G>A	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs751796325	T>A,C	Likely-benign, likely-pathogenic	Synonymous variant, missense variant, coding sequence variant
rs786205487	A>T	Likely-pathogenic	Stop gained, coding sequence variant
rs797045004	T>A	Pathogenic	Coding sequence variant, missense variant
rs863223314	->A	Pathogenic	Coding sequence variant, frameshift variant
rs864622083	C>A	Likely-pathogenic	Coding sequence variant, missense variant
rs864622269	C>T	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs864622520	G>A	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs886041897	T>C	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs1064795212	G>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1555364149	C>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1555364153	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1555364246	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1555364247	A>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1555365509	C>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs1555365597	C>A	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs1555365850	T>C	Pathogenic	Coding sequence variant, missense variant
rs1555365854	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1566733927	A>-,AA	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1566735903	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1595600383	T>A,C	Pathogenic	Missense variant, coding sequence variant
rs1595619553	G>-	Uncertain-significance, pathogenic	Frameshift variant, coding sequence variant
rs1595621310	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1595621335	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1595625010	T>C	Pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs1595625099	AGA>-	Likely-pathogenic	Inframe deletion, coding sequence variant
rs1595625104	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1595625113	T>C	Pathogenic	Missense variant, coding sequence variant
rs1595625206	AAT>-	Pathogenic	Inframe deletion, coding sequence variant

Show/Hide all (16)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018361	hsa-miR-335-5p	Microarray	18185580
MIRT021430	hsa-miR-9-5p	Microarray	17612493
MIRT051409	hsa-let-7f-5p	CLASH	23622248
MIRT805782	hsa-miR-1272	CLIP-seq
MIRT805783	hsa-miR-1322	CLIP-seq
MIRT805784	hsa-miR-370	CLIP-seq
MIRT805785	hsa-miR-3942-5p	CLIP-seq
MIRT805786	hsa-miR-4424	CLIP-seq
MIRT805787	hsa-miR-4495	CLIP-seq
MIRT805788	hsa-miR-4663	CLIP-seq
MIRT805789	hsa-miR-4682	CLIP-seq
MIRT805790	hsa-miR-4703-5p	CLIP-seq
MIRT805791	hsa-miR-3914	CLIP-seq
MIRT805782	hsa-miR-1272	CLIP-seq
MIRT805783	hsa-miR-1322	CLIP-seq
MIRT1545602	hsa-miR-495	CLIP-seq

Show/Hide all (34)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0000166	Function	Nucleotide binding	IEA
GO:0003924	Function	GTPase activity	IBA
GO:0003924	Function	GTPase activity	IEA
GO:0005515	Function	Protein binding	IPI	16815977, 19665976, 20200447, 23969831, 25751282, 32814053
GO:0005525	Function	GTP binding	IBA
GO:0005525	Function	GTP binding	IEA
GO:0005525	Function	GTP binding	ISS
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA	19665976
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	ISS
GO:0005794	Component	Golgi apparatus	IEA
GO:0005794	Component	Golgi apparatus	ISS
GO:0007029	Process	Endoplasmic reticulum organization	IBA
GO:0007409	Process	Axonogenesis	ISS
GO:0016020	Component	Membrane	IEA
GO:0016320	Process	Endoplasmic reticulum membrane fusion	IDA	38509071
GO:0016320	Process	Endoplasmic reticulum membrane fusion	IMP	27619977
GO:0016787	Function	Hydrolase activity	IEA
GO:0030424	Component	Axon	IEA
GO:0042802	Function	Identical protein binding	IDA	14506257
GO:0042802	Function	Identical protein binding	IPI	21220294, 21368113, 22802620, 23334294
GO:0042995	Component	Cell projection	IEA
GO:0051260	Process	Protein homooligomerization	IBA
GO:0051260	Process	Protein homooligomerization	IEA
GO:0071782	Component	Endoplasmic reticulum tubular network	IEA
GO:0071782	Component	Endoplasmic reticulum tubular network	ISS
GO:0098826	Component	Endoplasmic reticulum tubular network membrane	IDA	27619977
GO:0098827	Component	Endoplasmic reticulum subcompartment	IEA
GO:0140523	Function	GTPase-dependent fusogenic activity	IDA	38509071
GO:1990674	Component	Golgi cis cisterna membrane	ISS
GO:1990809	Process	Endoplasmic reticulum tubular network membrane organization	IMP	19665976, 27619977, 38509071

MIM	HGNC	e!Ensembl
606439	11231	ENSG00000198513

Q8WXF7

Protein name

Atlastin-1 (ATL-1) (EC 3.6.5.-) (Brain-specific GTP-binding protein) (GTP-binding protein 3) (GBP-3) (hGBP3) (Guanine nucleotide-binding protein 3) (Spastic paraplegia 3 protein A)

Protein function

Atlastin-1 (ATL1) is a membrane-anchored GTPase that mediates the GTP-dependent fusion of endoplasmic reticulum (ER) membranes, maintaining the continuous ER network. It facilitates the formation of three-way junctions where ER tubules intersect

PDB

3Q5D , 3Q5E , 3QNU , 3QOF , 4IDN , 4IDO , 4IDP , 4IDQ , 6B9D , 6B9E , 6B9F , 6B9G , 6XJN , 7OL3

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02263	GBP	43 → 314	Guanylate-binding protein, N-terminal domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed predominantly in the adult and fetal central nervous system. Measurable expression in all tissues examined, although expression in adult brain is at least 50-fold higher than in other tissues. Detected predominantly in pyrami

Sequence

MAKNRRDRNSWGGFSEKTYEWSSEEEEPVKKAGPVQVLIVKDDHSFELDETALNRILLSE
AVRDKEVVAVSVAGAFRKGKSFLMDFMLRYMYNQESVDWVGDYNEPLTGFSWRGGSERET
TGIQIWSEIFLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQ
NVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRL
KVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKIL
IPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSMLQATAEANNLAAV
ATAKDTYNKKMEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKMGGEEFSRRYLQQ
LESEIDELYIQYIKHNDSKNIFHAARTPATLFVVIFITYVIAGVTGFIGLDIIASLCNMI
MGLTLITLCTWAYIRYSGEYRELGAVIDQVAAALWDQGSTNEALYKLYSAAATHRHLYHQ
AFPTPKSESTEQSEKKKM

Sequence length

558

Interactions

View interactions

596

Show/Hide Causal Diseases (13)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the nervous system	Likely pathogenic	rs1064795212	RCV001814486
Accessory ectopic thyroid tissue	Likely pathogenic	rs1595625104	RCV001849513
ATL1-related spastic paraplegia, recessive	Pathogenic	rs1316385532	RCV005253870
Charcot-Marie-Tooth disease	Pathogenic	rs1555365597	RCV000789726
Distal lower limb muscle weakness	Pathogenic	rs1555365597	RCV000626932
Distal sensory impairment	Pathogenic	rs1555365597	RCV000626932
Hereditary spastic paraplegia	Likely pathogenic; Pathogenic	rs119476046, rs1595625206, rs864622520, rs864622269, rs2504540656, rs1595625099	RCV001847579 RCV001847580 RCV001847933 RCV001847927 RCV003229541 RCV001847131
Hereditary spastic paraplegia 3A	Likely pathogenic; Pathogenic	rs2140205438, rs1595621292, rs1595625104, rs2140208127, rs119476048, rs2140205448, rs606231265, rs2140205433, rs2504493603, rs786205487, rs119476046, rs119476047, rs119476049, rs28939094, rs119476050 View all (42 more)	RCV001360017 RCV001379963 RCV001379692 RCV001385343 RCV001970209 RCV002030577 RCV002514782 RCV002248974 RCV002470667 RCV003987402 RCV000004594 RCV000004595 RCV000004596 RCV000004597 RCV000004599 RCV000004600 RCV000004601 RCV000004602 RCV002807138 RCV000190502 RCV002862650 RCV002882206 RCV003026230 RCV000206078 RCV000203941 RCV000203724 RCV003153130 RCV003320400 RCV003312908 RCV003312911 RCV003312913 RCV003312915 RCV003384313 RCV003502917 RCV003612879 RCV003613515 RCV000020721 RCV002526601 RCV002527456 RCV000556273 RCV000536383 RCV000647936 RCV000698465 RCV000761255 RCV000810038 RCV000793809 RCV000793973 RCV000989218 RCV000989219 RCV000995703 RCV001027705 RCV001065616 RCV001223499 RCV001251114 RCV001261529 RCV001391396 RCV001391389 RCV001391390 RCV001391391 RCV001391392 RCV001391394 RCV001391395 RCV001391449
Neurodevelopmental delay	Likely pathogenic	rs2140233513, rs2140233530	RCV002274317 RCV002274318
Neuropathy, hereditary sensory, type 1D	Likely pathogenic; Pathogenic	rs119476046, rs1555365597, rs1566733927	RCV000850530 RCV000023542 RCV000791019
Osteomyelitis leading to amputation due to slow healing fractures	Pathogenic	rs1555365597	RCV000626932
Penetrating foot ulcers	Pathogenic	rs1555365597	RCV000626932
Spastic paraplegia	Likely pathogenic; Pathogenic	rs119476046	RCV001003978

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Abnormal pyramidal sign	Conflicting classifications of pathogenicity	rs1060502971	RCV001526629
Acute myeloid leukemia	Uncertain significance	rs886050531	RCV005929299
Adrenocortical carcinoma, hereditary	Benign	rs35014209	RCV005887595
ATL1-related disorder	Likely benign; Benign; Uncertain significance; Conflicting classifications of pathogenicity	rs765171869, rs3759588, rs2504564196, rs186528086, rs951568761, rs147839037, rs76375909, rs146975855, rs139720661	RCV003930921 RCV003982898 RCV003403782 RCV003947533 RCV003397779 RCV003409489 RCV003940214 RCV003910175 RCV003910176
Colorectal cancer	Benign	rs35014209	RCV005887596
Gastric cancer	Benign	rs753642042	RCV005868640
Lingual thyroid	Uncertain significance	rs2140234783	RCV001849809
Lymphoma	Likely benign	rs140173855	RCV005905373
Ovarian serous cystadenocarcinoma	Likely benign	rs140173855	RCV005905374
See cases	Uncertain significance	rs2039484269	RCV004584447
Spastic paraplegia, autosomal dominant	Conflicting classifications of pathogenicity	rs753145983	RCV000333856

Show/Hide Text Mining Associations (41)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alcoholic Neuropathy	Associate	36359747
Alzheimer Disease	Associate	22817815
Amyotrophic Lateral Sclerosis	Associate	30778698
Aneurysm	Associate	36717793
Ataxia	Associate	30778698
Bulbar Palsy Progressive	Associate	35925862
Carcinoma Hepatocellular	Associate	36423520, 36893885, 39516467
Carcinoma Non Small Cell Lung	Associate	37633973
Cerebral Palsy	Associate	35076175
Cholesterol pneumonia	Associate	33287888
Colorectal Neoplasms	Associate	23298232, 36209353
Dystonia	Associate	34808209
Esophageal Squamous Cell Carcinoma	Associate	36576648
Fetal Alcohol Spectrum Disorders	Associate	35925862
Fragile X Syndrome	Associate	10677308
Idiopathic Pulmonary Fibrosis	Associate	32378592
Intracranial Aneurysm	Associate	36717793
Intrauterine Growth Retardation Metaphyseal Dysplasia Adrenal Hypoplasia Congenita And Genital Anomalies	Associate	35925862
Liver Cirrhosis	Associate	30592264
Lung Neoplasms	Associate	35256587, 35459868, 36264074, 37903990
Lymphoma Large B Cell Diffuse	Associate	37294920, 38311062
Motor Neuron Disease	Associate	36359747
Neoplasms	Associate	23298232, 30922247, 37633973
Neoplasms	Inhibit	35256587
Nerve Degeneration	Associate	33287888
Nervous System Diseases	Associate	34782662
Neurodegenerative Diseases	Associate	21220294
Neuronopathy Distal Hereditary Motor Type V	Associate	22703882
O'Donnell Pappas syndrome	Associate	38634365
Osteogenesis imperfecta type 1A	Stimulate	36717793
Paraplegia	Associate	19573020, 19652243, 20932283
Peripheral Nervous System Diseases	Associate	35925862
Quadriplegia	Associate	34808209
Spastic paraplegia 3 autosomal dominant	Associate	19085270, 19573020, 19652243, 24473461
Spastic paraplegia 4 autosomal dominant	Associate	7825576, 9847083
Spastic Paraplegia Hereditary	Associate	16339213, 18644145, 19085270, 19494379, 19652243, 20932283, 21220294, 21368113, 22703882, 22817815, 23969831, 25421405, 26600529, 27601211, 30778698 View all (6 more)
Spinocerebellar Ataxias	Associate	30778698
Spondylitis Ankylosing	Stimulate	38634365
Stevens Johnson Syndrome	Associate	39897035
Stomach Neoplasms	Associate	35691615, 39273151
Upper Extremity Deformities Congenital	Associate	35925862

ATL1 (atlastin GTPase 1)