RAB28

RAB28, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 4:13361354-13484365

Links

ENSG00000157869 ∙ NCBI:9364 ∙ OMIM:612994 ∙ HGNC:9768 ∙ Uniprot:P51157 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cone-rod dystrophy 18 (Strong), mode of inheritance: AR
• cone-rod dystrophy (Supportive), mode of inheritance: AD
• cone-rod dystrophy 18 (Definitive), mode of inheritance: AR
• RAB28-related retinopathy (Definitive), mode of inheritance: AR
• cone-rod dystrophy 18 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cone-rod dystrophy 18	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	23746546; 25356532

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAB28 gene.

• not_provided (164 variants)
• not_specified (20 variants)
• Retinal_dystrophy (10 variants)
• Cone-rod_dystrophy_18 (10 variants)
• Cone-rod_dystrophy (2 variants)
• RAB28-related_disorder (2 variants)
• Optic_atrophy (1 variants)
• Cone_dystrophy (1 variants)
• Retinitis_pigmentosa (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB28 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001017979.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	34		35
missense		3	64			67
nonsense	2					2
start loss			1			1
frameshift	8	2	1			11
splice donor/acceptor (+/-2bp)	1	1				2
Total	11	6	67	34	0

Highest pathogenic variant AF is 0.0000155281

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB28	protein_coding	protein_coding	ENST00000330852	7	123012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0249	0.963	125722	0	25	125747	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.377	101	112	0.900	0.00000522	1442
Missense in Polyphen		35	36.331	0.96337		480
Synonymous	-0.224	42	40.2	1.04	0.00000195	391
Loss of Function	2.20	5	13.8	0.362	6.68e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000367	0.000363
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000129	0.000123
Middle Eastern	0.000111	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.789
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.253
• ghis: 0.669

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rab28

Gene ontology

• Biological process: intracellular protein transport;Rab protein signal transduction;toxin transport
• Cellular component: cytoplasm;plasma membrane;ciliary rootlet;ciliary basal body
• Molecular function: GTPase activity;GTP binding;GDP binding