ATL2

atlastin GTPase 2, the group of Atlastins

Basic information

Region (hg38): 2:38293954-38377285

Previous symbols: [ "ARL6IP2" ]

Links

ENSG00000119787

∙ NCBI:64225 ∙ OMIM:609368 ∙ HGNC:24047 ∙ Uniprot:Q8NHH9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATL2 gene.

not_specified (74 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATL2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001135673.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			74 clinvar	1 clinvar		75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	74	1	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATL2	protein_coding	protein_coding	ENST00000378954	13	82406

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0118	0.988	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.389	286	305	0.937	0.0000145	3832
Missense in Polyphen		42	81.138	0.51763		1023
Synonymous	-1.08	118	104	1.13	0.00000483	1070
Loss of Function	3.79	10	33.8	0.296	0.00000193	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000231
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000563	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000338	0.0000327
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: GTPase tethering membranes through formation of trans- homooligomers and mediating homotypic fusion of endoplasmic reticulum membranes. Functions in endoplasmic reticulum tubular network biogenesis (PubMed:18270207, PubMed:19665976, PubMed:27619977). {ECO:0000269|PubMed:18270207, ECO:0000269|PubMed:19665976, ECO:0000269|PubMed:27619977}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

loftool: 0.205
rvis_EVS: -0.07
rvis_percentile_EVS: 48.69

Haploinsufficiency Scores

pHI: 0.505
hipred: Y
hipred_score: 0.581
ghis: 0.553

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.0709

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Atl2
Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype;

Gene ontology

Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;endoplasmic reticulum organization;Golgi organization;protein homooligomerization;endoplasmic reticulum tubular network membrane organization
Cellular component: endoplasmic reticulum;membrane;integral component of membrane;endoplasmic reticulum tubular network membrane
Molecular function: GTPase activity;protein binding;GTP binding;identical protein binding