ATL2

protein-coding

atlastin GTPase 2, the group of Atlastins

Gene summary

Enables GTPase-dependent fusogenic activity. Involved in endoplasmic reticulum membrane fusion and endoplasmic reticulum tubular network membrane organization. Located in endoplasmic reticulum membrane. Is active in endoplasmic reticulum tubular network membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ARL6IP2

MANE transcript

NM_001135673.4

Inheritance

—

ClinVar variants

U:89B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr2:38,293,954-38,377,285

External References & Databases

Ensembl (ENSG00000119787)

Transcript & Mutation Effects

hg38 • Region Span ~83.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001135673.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			86 clinvar	2 clinvar		88
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	89	2	1	92

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001135673.4	RefSeq	NP_001129145.1	13	MANE Select
ENST00000378954.9	Ensembl	ENSP00000368237.4	13	MANE Select
NM_001308076.1	RefSeq	NP_001295005.1	13	Standard
NM_001330458.2	RefSeq	NP_001317387.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
endoplasmic reticulum organization
Golgi organization
protein homooligomerization
endoplasmic reticulum tubular network membrane organization

Molecular Function

GTPase activity
protein binding
GTP binding
identical protein binding

Cellular Component

endoplasmic reticulum
membrane
integral component of membrane
endoplasmic reticulum tubular network membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378954
Coding exons: 13
Length: 82406
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125747
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.389	286	305	0.937	0.0000145	3832
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00023	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000056	0.000053	rare
South Asian	0.000034	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.0709

Gene Damage Prediction

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