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

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 (8 variants)
• Cone-rod dystrophy 18 (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.

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			1	34	1	36
missense		1	69			70
nonsense	1					1
start loss			1			1
frameshift	7	2	3			12
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	1				2
splice region			5	9	1	15
non coding		2	2	23	9	36
Total	9	6	77	57	10

Highest pathogenic variant AF is 0.0000263

Variants in RAB28

This is a list of pathogenic ClinVar variants found in the RAB28 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-13368630-A-C		Retinal dystrophy • not specified	Uncertain significance (Aug 26, 2024)
4-13368640-T-G		not specified	Uncertain significance (Nov 07, 2023)
4-13368684-T-C			Benign (Jul 05, 2018)
4-13369754-C-T			Benign (Aug 08, 2021)
4-13369873-G-A		Retinal dystrophy	Uncertain significance (Jan 01, 2022)
4-13369876-C-T			Likely benign (Dec 24, 2020)
4-13369880-T-C			Uncertain significance (Apr 19, 2022)
4-13369884-C-T			Uncertain significance (Aug 05, 2022)
4-13369885-TG-AT			Uncertain significance (Jul 07, 2023)
4-13369888-A-C		Cone-rod dystrophy 18	Conflicting classifications of pathogenicity (Feb 24, 2022)
4-13369888-A-G			Likely benign (Jul 16, 2023)
4-13369888-AC-A			Uncertain significance (Feb 05, 2022)
4-13369899-T-C			Uncertain significance (Sep 11, 2019)
4-13369900-C-CT			Uncertain significance (Oct 04, 2022)
4-13369905-T-C			Uncertain significance (Dec 20, 2023)
4-13369910-G-A			Uncertain significance (Oct 02, 2021)
4-13369919-T-C			Uncertain significance (Aug 31, 2021)
4-13369923-TTTCTTCTTCCGGG-T			Pathogenic (Jan 24, 2024)
4-13369925-T-C			Uncertain significance (Aug 24, 2023)
4-13369932-C-A			Pathogenic (Jan 24, 2024)
4-13369933-C-T			Likely benign (Jul 05, 2022)
4-13369934-G-A			Uncertain significance (Oct 13, 2022)
4-13369939-C-T			Likely benign (May 05, 2022)
4-13369953-C-T			Uncertain significance (Aug 11, 2021)
4-13369954-C-T			Likely benign (Nov 28, 2023)

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