AQR

protein-coding

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

Gene summary

Enables 3'-5' RNA helicase activity and single-stranded RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of U2-type catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_014691.3

Inheritance

—

ClinVar variants

U:148B:4

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr15:34,851,782-34,969,742

External References & Databases

Ensembl (ENSG00000021776)

Transcript & Mutation Effects

hg38 • Region Span ~118.0 kb

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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 AQR variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 133

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

not providedTotal: 1

AQR-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014691.3. 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			5 clinvar			5
missense			139 clinvar	4 clinvar		143
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	148	4	0	152

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014691.3	RefSeq	NP_055506.1	35	MANE Select
ENST00000156471.10	Ensembl	ENSP00000156471.5	35	MANE Select
ENST00000543879.6	Ensembl	ENSP00000445700.2	19	Standard
ENST00000560117.1	Ensembl	ENSP00000453278.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Spliceosome - Homo sapiens (human)
DNA Repair
Metabolism of RNA
mRNA Splicing - Major Pathway
Formation of TC-NER Pre-Incision Complex

Biological Process

mRNA splicing, via spliceosome
transcription-coupled nucleotide-excision repair

Molecular Function

RNA binding
mRNA binding
helicase activity
protein binding
ATP binding

Cellular Component

nucleus
nucleoplasm
spliceosomal complex
membrane
U2-type catalytic step 2 spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000156471
Coding exons: 35
Length: 114309
Individuals with no LoFs: 124778
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 124802
p: 0.0000962

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.55	509	790	0.644	0.0000406	9813
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.00010	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0995

Intolerance Scores

LoFtool: 0.0781
RVIS EVS: -1.02
RVIS percentile EVS: 8.14

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.944

Gene Damage Prediction

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