GAR1

GAR1 ribonucleoprotein, the group of H/ACA ribonucleoprotein complex

Basic information

Region (hg38): 4:109815510-109824740

Previous symbols: [ "NOLA1" ]

Links

ENSG00000109534

∙ NCBI:54433 ∙ OMIM:606468 ∙ HGNC:14264 ∙ Uniprot:Q9NY12 ∙ 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 GAR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAR1 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			12 clinvar	1 clinvar		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in GAR1

This is a list of pathogenic ClinVar variants found in the GAR1 region.

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

Position	Phenotype	Significance	ClinVar
4-109816184-G-A	not specified	Uncertain significance (Mar 25, 2024)	3280703
4-109816251-C-G	not specified	Uncertain significance (Apr 08, 2024)	3280702
4-109816254-AGGTGGAGGCGGC-A	GAR1-related disorder	Likely benign (Dec 07, 2022)	3051644
4-109816261-G-A	not specified	Likely benign (Jan 31, 2022)	2274733
4-109816354-C-G	not specified	Uncertain significance (Jun 28, 2022)	2386101
4-109816364-C-T	not specified	Uncertain significance (May 03, 2023)	2508143
4-109817987-C-A	not specified	Uncertain significance (Apr 12, 2025)	4028248
4-109818017-A-G	not specified	Uncertain significance (Sep 12, 2023)	2622458
4-109818022-C-A	not specified	Uncertain significance (Apr 07, 2025)	4028247
4-109818034-G-C	not specified	Uncertain significance (Jan 19, 2025)	3852839
4-109818051-T-G	not specified	Uncertain significance (Aug 21, 2023)	2590247
4-109818079-C-T	not specified	Uncertain significance (Nov 25, 2024)	3518737
4-109819014-A-C	not specified	Uncertain significance (Sep 29, 2023)	3098324
4-109822405-G-A	not specified	Uncertain significance (Jun 24, 2022)	2296176
4-109822426-G-C	not specified	Uncertain significance (Feb 12, 2024)	3098325
4-109822482-A-G	not specified	Uncertain significance (Jun 07, 2024)	3280704
4-109823989-G-C	not specified	Uncertain significance (Dec 11, 2024)	3852840
4-109824424-G-A	not specified	Uncertain significance (Dec 15, 2023)	3098326

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAR1	protein_coding	protein_coding	ENST00000226796	6	9228

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.100	0.893	125717	0	5	125722	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.232	110	117	0.940	0.00000533	1349
Missense in Polyphen		29	29.998	0.96673		409
Synonymous	0.402	36	39.2	0.918	0.00000171	460
Loss of Function	2.37	4	13.3	0.300	7.28e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000915	0.0000913
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Required for ribosome biogenesis and telomere maintenance. Part of the H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ("psi") residues, which may serve to stabilize the conformation of rRNAs. May also be required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme. {ECO:0000269|PubMed:10757788, ECO:0000269|PubMed:15044956}.;
Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

pRec: 0.125

Intolerance Scores

loftool: 0.255
rvis_EVS: 0.35
rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

pHI: 0.159
hipred: Y
hipred_score: 0.794
ghis: 0.527

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.388

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gar1
Phenotype: homeostasis/metabolism phenotype;

Gene ontology

Biological process: snoRNA guided rRNA pseudouridine synthesis;telomere maintenance via telomerase
Cellular component: nuclear chromosome, telomeric region;fibrillar center;nucleus;nucleoplasm;telomerase holoenzyme complex;box H/ACA snoRNP complex;box H/ACA scaRNP complex;box H/ACA telomerase RNP complex
Molecular function: RNA binding;protein binding;box H/ACA snoRNA binding;telomerase RNA binding