GeneBe

AQR

aquarius intron-binding spliceosomal factor, the group of UPF1 like RNA helicases|Spliceosomal B complex|Spliceosomal Bact complex|Spliceosomal P complex|Spliceosomal C complex

Basic information

Region (hg38): 15:34851782-34969742

Links

ENSG00000021776 ∙ NCBI:9716 ∙ OMIM:610548 ∙ HGNC:29513 ∙ Uniprot:O60306 ∙ 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 AQR gene.

  • not_specified (114 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
  • AQR-related_condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AQR gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014691.3. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
112
clinvar
4
clinvar
 116
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 112 4 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
AQRprotein_codingprotein_codingENST00000156471 35114309
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.000.000003941247780241248020.0000962
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.555097900.6440.00004069813
Missense in Polyphen102250.540.407113053
Synonymous0.009042622620.9990.00001272748
Loss of Function7.341183.30.1320.00000479980

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008750.0000875
Ashkenazi Jewish0.0002140.000199
East Asian0.00005560.0000556
Finnish0.000.00
European (Non-Finnish)0.0001260.000124
Middle Eastern0.00005560.0000556
South Asian0.0001050.0000980
Other0.0001670.000165

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:25599396, PubMed:28502770, PubMed:28076346). Intron-binding spliceosomal protein required to link pre-mRNA splicing and snoRNP (small nucleolar ribonucleoprotein) biogenesis (PubMed:16949364). Plays a key role in position-dependent assembly of intron-encoded box C/D small snoRNP, splicing being required for snoRNP assembly (PubMed:16949364). May act by helping the folding of the snoRNA sequence. Binds to intron of pre-mRNAs in a sequence-independent manner, contacting the region between snoRNA and the branchpoint of introns (40 nucleotides upstream of the branchpoint) during the late stages of splicing (PubMed:16949364). Has ATP-dependent RNA helicase activity and can unwind double-stranded RNA molecules with a 3' overhang (in vitro) (PubMed:25599396). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:16949364, ECO:0000269|PubMed:25599396, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770}.;
Pathway
Spliceosome - Homo sapiens (human);DNA Repair;Metabolism of RNA;mRNA Splicing - Major Pathway;Formation of TC-NER Pre-Incision Complex;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair (Consensus)

Recessive Scores

pRec
0.0995

Intolerance Scores

loftool
0.0781
rvis_EVS
-1.02
rvis_percentile_EVS
8.14

Haploinsufficiency Scores

pHI
0.139
hipred
Y
hipred_score
0.704
ghis
0.621

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.944

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Aqr
Phenotype
normal phenotype;

Gene ontology

Biological process
mRNA splicing, via spliceosome;transcription-coupled nucleotide-excision repair
Cellular component
nucleus;nucleoplasm;spliceosomal complex;membrane;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
Molecular function
RNA binding;mRNA binding;helicase activity;protein binding;ATP binding