AAR2

AAR2 splicing factor

Basic information

Region (hg38): 20:36236131-36270918

Previous symbols: [ "C20orf4" ]

Links

ENSG00000131043 ∙ NCBI:25980 ∙ OMIM:617365 ∙ HGNC:15886 ∙ Uniprot:Q9Y312 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• multiple congenital anomalies/dysmorphic syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AAR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AAR2 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				1		1
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in AAR2

This is a list of pathogenic ClinVar variants found in the AAR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-36239885-T-C		not specified	Uncertain significance (May 17, 2023)
20-36239888-A-C		not specified	Uncertain significance (Mar 08, 2025)
20-36239906-G-A		not specified	Uncertain significance (Jan 24, 2025)
20-36240002-T-G		not specified	Uncertain significance (Aug 20, 2024)
20-36240004-C-T		not specified	Uncertain significance (Dec 19, 2022)
20-36240005-G-A		not specified	Uncertain significance (Nov 03, 2022)
20-36240025-C-G		not specified	Uncertain significance (May 24, 2024)
20-36240079-G-C		not specified	Uncertain significance (Aug 14, 2024)
20-36240080-T-C		not specified	Uncertain significance (Dec 20, 2023)
20-36240136-C-T		not specified	Uncertain significance (Mar 11, 2025)
20-36240172-C-G		not specified	Uncertain significance (Apr 26, 2024)
20-36240173-C-A		not specified	Uncertain significance (Dec 10, 2024)
20-36240188-A-T		not specified	Uncertain significance (Aug 17, 2022)
20-36240208-A-G		not specified	Uncertain significance (Dec 02, 2024)
20-36240211-C-G		not specified	Uncertain significance (Oct 30, 2023)
20-36240215-A-T		not specified	Uncertain significance (Dec 14, 2022)
20-36240219-G-A			Likely benign (Mar 01, 2024)
20-36240302-T-C		not specified	Uncertain significance (Dec 10, 2024)
20-36240302-T-G		not specified	Uncertain significance (Apr 04, 2024)
20-36240330-G-C		not specified	Uncertain significance (Jan 09, 2025)
20-36240344-C-G		not specified	Uncertain significance (Aug 29, 2024)
20-36240386-G-A		not specified	Uncertain significance (Sep 30, 2024)
20-36240388-G-A		8 conditions	Likely pathogenic (Jan 10, 2016)
20-36240406-C-T		not specified	Uncertain significance (Mar 14, 2025)
20-36240407-G-A		not specified	Uncertain significance (Feb 12, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AAR2	protein_coding	protein_coding	ENST00000373932	3	34460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000831	0.535	125553	0	195	125748	0.000776

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.855	190	226	0.840	0.0000135	2535
Missense in Polyphen		66	86.022	0.76724		995
Synonymous	0.790	83	92.7	0.896	0.00000552	772
Loss of Function	0.715	9	11.6	0.774	5.70e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000589	0.000589
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00129	0.00129
Middle Eastern	0.00	0.00
South Asian	0.000294	0.000294
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the U5 snRNP complex that is required for spliceosome assembly and for pre-mRNA splicing. {ECO:0000250|UniProtKB:P32357}.

Recessive Scores

• pRec: 0.0869

Intolerance Scores

• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.06

Haploinsufficiency Scores

• pHI: 0.0837
• hipred: N
• hipred_score: 0.197
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aar2

Gene ontology

• Biological process: spliceosomal tri-snRNP complex assembly
• Cellular component: spliceosomal complex