RABGAP1L

RAB GTPase activating protein 1 like

Basic information

Region (hg38): 1:174159409-174995308

Links

ENSG00000152061 ∙ NCBI:9910 ∙ OMIM:609238 ∙ HGNC:24663 ∙ Uniprot:B7ZAP0, Q5R372 ∙ 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 RABGAP1L gene.

• Inborn genetic diseases (29 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABGAP1L 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					2	2
missense			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8		1	9
Total	0	0	31	0	4

Variants in RABGAP1L

This is a list of pathogenic ClinVar variants found in the RABGAP1L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-174184147-G-A		Cholesteatoma	Likely pathogenic (-)
1-174219198-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-174221032-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-174221067-A-G			Benign (Jun 01, 2022)
1-174221071-T-G		not specified	Uncertain significance (Jan 03, 2024)
1-174231231-A-G		not specified	Uncertain significance (Dec 19, 2023)
1-174231283-C-A		not specified	Uncertain significance (Oct 26, 2021)
1-174241526-A-G			Uncertain significance (Dec 01, 2021)
1-174241530-A-G		not specified	Uncertain significance (Mar 16, 2022)
1-174241532-A-G		not specified	Uncertain significance (Sep 15, 2022)
1-174241548-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-174241554-G-C		not specified	Uncertain significance (Dec 06, 2021)
1-174241566-C-T		not specified	Uncertain significance (Nov 09, 2021)
1-174241652-G-C		not specified	Uncertain significance (Dec 16, 2023)
1-174250512-A-G		not specified	Uncertain significance (Oct 22, 2021)
1-174250548-C-T		not specified	Uncertain significance (May 18, 2022)
1-174250560-C-A		not specified	Uncertain significance (Dec 20, 2022)
1-174250587-G-T		not specified	Uncertain significance (Oct 04, 2022)
1-174252533-A-G		not specified	Uncertain significance (Dec 20, 2023)
1-174272448-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-174275914-C-T			Uncertain significance (Apr 01, 2022)
1-174278700-G-T		not specified	Uncertain significance (Oct 26, 2022)
1-174278748-T-C		not specified	Uncertain significance (Aug 11, 2022)
1-174305008-A-T		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
1-174305044-A-G		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABGAP1L	protein_coding	protein_coding	ENST00000251507	20	835898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000109	1.00	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	360	425	0.847	0.0000210	5376
Missense in Polyphen		102	136.98	0.74466		1721
Synonymous	0.168	151	154	0.983	0.00000801	1488
Loss of Function	4.25	16	47.7	0.335	0.00000258	576

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000576	0.000573
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000117	0.000109
Finnish	0.0000475	0.0000462
European (Non-Finnish)	0.000219	0.000202
Middle Eastern	0.000117	0.000109
South Asian	0.0000989	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.376
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.11

Haploinsufficiency Scores

• pHI: 0.379
• hipred: N
• hipred_score: 0.492
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rabgap1l
• Phenotype: normal phenotype

Gene ontology

• Biological process: intracellular protein transport;endocytosis;regulation of protein localization;activation of GTPase activity
• Cellular component: nucleus;early endosome;Golgi apparatus
• Molecular function: GTPase activator activity;Rab GTPase binding