RAB42

RAB42, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 1:28592199-28595449

Links

ENSG00000188060 ∙ NCBI:115273 ∙ ∙ HGNC:28702 ∙ Uniprot:Q8N4Z0 ∙ 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 RAB42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB42 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in RAB42

This is a list of pathogenic ClinVar variants found in the RAB42 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-28592578-A-C		not specified	Uncertain significance (Jun 18, 2021)
1-28592614-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-28592637-G-C		not specified	Uncertain significance (Jan 22, 2024)
1-28592692-G-A		not specified	Uncertain significance (Jun 13, 2022)
1-28593717-G-A		not specified	Uncertain significance (Jun 28, 2023)
1-28593781-A-C		not specified	Uncertain significance (Nov 09, 2023)
1-28593906-C-T		not specified	Uncertain significance (May 14, 2024)
1-28593929-G-C		not specified	Uncertain significance (Aug 16, 2022)
1-28594032-G-T		not specified	Uncertain significance (Nov 28, 2023)
1-28594053-T-C		not specified	Uncertain significance (Aug 04, 2023)
1-28594075-G-T		not specified	Uncertain significance (Feb 05, 2024)
1-28594077-C-A		not specified	Uncertain significance (May 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB42	protein_coding	protein_coding	ENST00000373826	1	3244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00297	0.376	125684	0	11	125695	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.108	62	59.6	1.04	0.00000327	673
Missense in Polyphen		23	20.136	1.1422		223
Synonymous	0.766	22	27.1	0.813	0.00000156	214
Loss of Function	-0.797	3	1.83	1.64	7.81e-8	20

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000245
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Intolerance Scores

• loftool: 0.708
• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.92

Haploinsufficiency Scores

• pHI: 0.0925
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab42

Gene ontology

• Cellular component: membrane
• Molecular function: GTPase activity;GTP binding