ABCE1

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

Basic information

Region (hg38): 4:145098287-145129524

Previous symbols: [ "RNASEL1", "RNASELI", "RNS4I" ]

Links

ENSG00000164163 ∙ NCBI:6059 ∙ OMIM:601213 ∙ HGNC:69 ∙ Uniprot:P61221 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCE1 gene.

• Inborn genetic diseases (6 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCE1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					3	3
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	5	1	3

Variants in ABCE1

This is a list of pathogenic ClinVar variants found in the ABCE1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-145104421-C-G		not specified	Uncertain significance (May 04, 2023)
4-145109158-T-C		not specified	Uncertain significance (Sep 17, 2021)
4-145109174-A-T			Benign (Apr 04, 2018)
4-145110426-A-G		not specified	Likely benign (Jan 27, 2022)
4-145110451-G-T			Benign (Jan 19, 2018)
4-145111042-G-A		not specified	Uncertain significance (Feb 22, 2023)
4-145111062-T-G		Malignant tumor of prostate	Uncertain significance (-)
4-145112254-G-A			Benign (Apr 04, 2018)
4-145119934-A-G		not specified	Uncertain significance (Jun 06, 2023)
4-145120042-A-T		not specified	Uncertain significance (Aug 13, 2021)
4-145123265-C-T			Benign (Apr 04, 2018)
4-145123482-A-G		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCE1	protein_coding	protein_coding	ENST00000296577	17	31248

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.974	0.0262	125731	0	14	125745	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.10	112	318	0.353	0.0000161	3912
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000330	0.000323
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.315

Intolerance Scores

• loftool: 0.0985
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.549
• hipred: Y
• hipred_score: 0.783
• ghis: 0.719

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.851

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abce1
• 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)

Zebrafish Information Network

• Gene name: abce1
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: ribosomal subunit export from nucleus;translational initiation;translational termination;viral process;defense response to virus;regulation of type I interferon-mediated signaling pathway;negative regulation of endoribonuclease activity
• Cellular component: cytoplasm;mitochondrion;mitochondrial matrix;cytosol;membrane
• Molecular function: iron ion binding;protein binding;ATP binding;ATPase activity;ribosomal small subunit binding;endoribonuclease inhibitor activity