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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (13)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the nervous system	Likely pathogenic	rs1064795212	RCV001814486	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Accessory ectopic thyroid tissue	Likely pathogenic	rs1595625104	RCV001849513	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
ATL1-related spastic paraplegia, recessive	Pathogenic	rs1316385532	RCV005253870	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Charcot-Marie-Tooth disease	Pathogenic	rs1555365597	RCV000789726	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Distal lower limb muscle weakness	Pathogenic	rs1555365597	RCV000626932	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Distal sensory impairment	Pathogenic	rs1555365597	RCV000626932	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hereditary spastic paraplegia	Likely pathogenic; Pathogenic	rs119476046, rs1595625206, rs864622520, rs864622269, rs2504540656, rs1595625099	RCV001847579 RCV001847580 RCV001847933 RCV001847927 RCV003229541 RCV001847131 View all (1 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
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 View all (58 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental delay	Likely pathogenic	rs2140233513, rs2140233530	RCV002274317 RCV002274318	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neuropathy, hereditary sensory, type 1D	Likely pathogenic; Pathogenic	rs119476046, rs1555365597, rs1566733927	RCV000850530 RCV000023542 RCV000791019	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Osteomyelitis leading to amputation due to slow healing fractures	Pathogenic	rs1555365597	RCV000626932	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Penetrating foot ulcers	Pathogenic	rs1555365597	RCV000626932	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spastic paraplegia	Likely pathogenic; Pathogenic	rs119476046	RCV001003978	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (21)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Abnormal pyramidal sign	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Acute myeloid leukemia	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATL1-related disorder	Likely benign; Benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL DOMINANT SPASTIC PARAPLEGIA TYPE 3	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIOVASCULAR DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL NEUROLOGIC ANOMALIES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DUPUYTREN CONTRACTURE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY SENSORY AND AUTONOMIC NEUROPATHY TYPE 1	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY SENSORY AUTONOMIC NEUROPATHY, TYPE 1	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lingual thyroid	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROPATHY, HEREDITARY SENSORY, TYPE ID	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POTASSIUM DEFICIENCY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA 3, AUTOSOMAL DOMINANT	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spastic paraplegia, autosomal dominant	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPASTIC PARAPLEGIA, HEREDITARY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (18)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acidosis Lactic	Lactic acidosis	Pubtator	25434004	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Basal Cell Nevus Syndrome	Basal cell nevus syndrome	Pubtator	29081410	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	25434004	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	37551111	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	37161254	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	37161254	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathy Hypertrophic	Hypertrophic cardiomyopathy	Pubtator	25434004	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	29128363		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	37161254	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hashimoto Disease	Hashimoto disease	Pubtator	37545519	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leigh Disease	Leigh syndrome	Pubtator	25434004	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Melanoma	Pubtator	37161254	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	25434004	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	29128363		★★★★★ ★☆☆☆☆ Found in Text Mining only
Polycystic Ovary Syndrome	Polycystic ovary syndrome	Pubtator	37545519	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	Pubtator	37161254	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	37161254	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uveal melanoma	Uveal melanoma	Pubtator	37161254	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

ATL1 (atlastin GTPase 1)