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): 15:34851781-34969742

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.

• Inborn genetic diseases (28 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.

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						0
missense			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	0

Variants in AQR

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

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

Position	Type	Phenotype	Significance	ClinVar
15-34856907-G-A		not specified	Uncertain significance (Dec 19, 2022)
15-34856955-G-C		not specified	Uncertain significance (Jan 03, 2022)
15-34856970-C-T		not specified	Uncertain significance (Mar 01, 2023)
15-34856981-G-T		not specified	Uncertain significance (Jun 09, 2022)
15-34857006-G-C		not specified	Uncertain significance (Nov 22, 2021)
15-34857070-C-T		not specified	Likely benign (Feb 27, 2024)
15-34860074-G-A		not specified	Uncertain significance (Apr 25, 2022)
15-34862878-T-C		not specified	Uncertain significance (Aug 22, 2022)
15-34862901-A-G		not specified	Uncertain significance (Jan 30, 2024)
15-34870862-G-A		not specified	Uncertain significance (Oct 29, 2021)
15-34873832-T-A		not specified	Uncertain significance (Feb 05, 2024)
15-34873832-T-C		not specified	Uncertain significance (Jul 30, 2023)
15-34873950-G-A		not specified	Uncertain significance (Nov 13, 2023)
15-34873981-G-C		not specified	Uncertain significance (Aug 16, 2022)
15-34884581-T-C		not specified	Uncertain significance (Dec 14, 2023)
15-34884663-T-A		not specified	Uncertain significance (Jan 23, 2023)
15-34886632-C-T		not specified	Uncertain significance (Dec 03, 2021)
15-34893751-C-A		not specified	Uncertain significance (Jun 22, 2023)
15-34896959-T-C		not specified	Uncertain significance (Feb 28, 2023)
15-34897560-G-A		not specified	Uncertain significance (Jul 20, 2022)
15-34897623-T-C		not specified	Uncertain significance (Jul 06, 2022)
15-34897635-C-T		not specified	Uncertain significance (Feb 28, 2023)
15-34897661-T-A		not specified	Uncertain significance (Jan 02, 2024)
15-34900698-G-A		not specified	Uncertain significance (Apr 11, 2023)
15-34900745-T-C		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AQR	protein_coding	protein_coding	ENST00000156471	35	114309

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000394	124778	0	24	124802	0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.55	509	790	0.644	0.0000406	9813
Missense in Polyphen		102	250.54	0.40711		3053
Synonymous	0.00904	262	262	0.999	0.0000127	2748
Loss of Function	7.34	11	83.3	0.132	0.00000479	980

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000875	0.0000875
Ashkenazi Jewish	0.000214	0.000199
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000126	0.000124
Middle Eastern	0.0000556	0.0000556
South Asian	0.000105	0.0000980
Other	0.000167	0.000165

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

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

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