GARNL3

GTPase activating Rap/RanGAP domain like 3

Basic information

Region (hg38): 9:127224265-127393660

Links

ENSG00000136895 ∙ NCBI:84253 ∙ ∙ HGNC:25425 ∙ Uniprot:Q5VVW2 ∙ 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 GARNL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GARNL3 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	31	1	0

Variants in GARNL3

This is a list of pathogenic ClinVar variants found in the GARNL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127264927-T-C		not specified	Uncertain significance (Nov 17, 2023)
9-127264963-A-C		not specified	Uncertain significance (Nov 15, 2021)
9-127313524-G-A		not specified	Uncertain significance (May 27, 2022)
9-127313542-A-G		not specified	Uncertain significance (May 18, 2023)
9-127318064-G-A		not specified	Uncertain significance (Oct 27, 2022)
9-127325072-T-A		not specified	Uncertain significance (May 01, 2024)
9-127333026-T-C		not specified	Uncertain significance (May 02, 2024)
9-127333080-T-C			Uncertain significance (Aug 01, 2024)
9-127333101-G-A		not specified	Uncertain significance (Oct 07, 2022)
9-127335259-A-T		not specified	Uncertain significance (May 29, 2024)
9-127335329-A-G		Intellectual disability	Likely pathogenic (-)
9-127338116-A-G		not specified	Uncertain significance (Apr 04, 2024)
9-127339698-C-T		not specified	Uncertain significance (May 25, 2022)
9-127342261-C-G		not specified	Uncertain significance (Oct 26, 2021)
9-127342272-C-T		not specified	Uncertain significance (Mar 26, 2024)
9-127342326-T-A		not specified	Uncertain significance (Jul 15, 2021)
9-127344311-G-A		not specified	Uncertain significance (May 24, 2023)
9-127348925-C-T		not specified	Uncertain significance (Dec 16, 2022)
9-127349020-G-A		not specified	Uncertain significance (May 23, 2024)
9-127353899-C-T		not specified	Uncertain significance (Sep 22, 2022)
9-127354371-A-G		not specified	Uncertain significance (May 31, 2023)
9-127355446-C-T		not specified	Uncertain significance (Oct 20, 2023)
9-127357258-G-A		not specified	Uncertain significance (May 14, 2024)
9-127357306-C-G		not specified	Uncertain significance (Sep 26, 2023)
9-127357337-C-T		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GARNL3	protein_coding	protein_coding	ENST00000373387	28	169396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000689	1.00	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	435	571	0.762	0.0000313	6635
Missense in Polyphen		143	213.62	0.66943		2407
Synonymous	-0.509	227	217	1.04	0.0000127	1983
Loss of Function	4.62	20	58.0	0.345	0.00000304	691

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000334	0.000334
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000218	0.000217
South Asian	0.0000984	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.173
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.24

Haploinsufficiency Scores

• pHI: 0.326
• hipred: Y
• hipred_score: 0.682
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.387

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Garnl3

Gene ontology

• Biological process: positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: intracellular membrane-bounded organelle
• Molecular function: GTPase activator activity