ABCE1

protein-coding

ATP binding cassette subfamily E member 1, the group of ATP binding cassette subfamily E

Gene summary

The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the OABP subfamily. Alternatively referred to as the RNase L inhibitor, this protein functions to block the activity of ribonuclease L. Activation of ribonuclease L leads to inhibition of protein synthesis in the 2-5A/RNase L system, the central pathway for viral interferon action. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

RNASEL1
RNASELI
RNS4I

MANE transcript

NM_002940.3

Inheritance

—

ClinVar variants

U:34B:5

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr4:145,098,288-145,129,524

External References & Databases

Ensembl (ENSG00000164163)

Transcript & Mutation Effects

hg38 • Region Span ~31.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABCE1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 25

not providedTotal: 6

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002940.3. 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			1 clinvar		3 clinvar	4
missense			30 clinvar	2 clinvar		32
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	34	2	3	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002940.3	RefSeq	NP_002931.2	17	MANE Select
ENST00000296577.9	Ensembl	ENSP00000296577.4	17	MANE Select
NM_001040876.2	RefSeq	NP_001035809.1	17	Standard
ENST00000502586.5	Ensembl	ENSP00000421250.1	7	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
abce1	Danio rerio	Structure: head Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

abce1

Danio rerio

Structure: head

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cytokine Signaling in Immune system
Immune System
Interferon alpha/beta signaling
Interferon Signaling

Biological Process

ribosomal subunit export from nucleus
translational initiation
translational termination
viral process
defense response to virus

Molecular Function

iron ion binding
protein binding
ATP binding
ATPase activity
ribosomal small subunit binding

Cellular Component

cytoplasm
mitochondrion
mitochondrial matrix
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296577
Coding exons: 17
Length: 31248
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125745
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.10	112	318	0.353	0.0000161	3912
Missense (PolyPhen)		19	117.17	0.16216		1477
Synonymous	0.933	93	105	0.884	0.00000543	1106
Loss of Function	4.78	6	37.7	0.159	0.00000221	449

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Antagonizes the binding of 2-5A (5'-phosphorylated 2',5'-linked oligoadenylates) by RNase L through direct interaction with RNase L and therefore inhibits its endoribonuclease activity. May play a central role in the regulation of mRNA turnover. Antagonizes the anti-viral effect of the interferon-regulated 2-5A/RNase L pathway. May act as a chaperone for post-translational events during HIV-1 capsid assembly. {ECO:0000269|PubMed:11585831, ECO:0000269|PubMed:9660177, ECO:0000269|PubMed:9847332}.;

Recessive Scores

pRec: 0.315

Intolerance Scores

LoFtool: 0.0985
RVIS EVS: -0.25
RVIS percentile EVS: 35.42

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.851

Gene Damage Prediction

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