GORAB

golgin, RAB6 interacting

Basic information

Region (hg38): 1:170531818-170553834

Previous symbols: [ "SCYL1BP1" ]

Links

ENSG00000120370 ∙ NCBI:92344 ∙ OMIM:607983 ∙ HGNC:25676 ∙ Uniprot:Q5T7V8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• geroderma osteodysplastica (Definitive), mode of inheritance: AR
• geroderma osteodysplastica (Moderate), mode of inheritance: AR
• geroderma osteodysplastica (Strong), mode of inheritance: AR
• geroderma osteodysplastica (Strong), mode of inheritance: AR
• geroderma osteodysplastica (Moderate), mode of inheritance: AR
• geroderma osteodysplastica (Strong), mode of inheritance: AR
• geroderma osteodysplastica (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Geroderma osteodysplasticum	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	Dermatologic; Musculoskeletal	631850; 474638; 3236370; 8213917; 8723088; 9018419; 18997784; 18348262; 19681135; 21204221

ClinVar

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

• not provided (216 variants)
• Geroderma osteodysplastica (86 variants)
• Inborn genetic diseases (24 variants)
• not specified (5 variants)
• GORAB-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GORAB 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	44	4	49
missense			90	4	1	95
nonsense	7	1	3			11
start loss			1			1
frameshift	10	4	1			15
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region			1	2	1	4
non coding	1		36	26	16	79
Total	19	5	132	74	21

Highest pathogenic variant AF is 0.0000263

Variants in GORAB

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

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

Position	Type	Phenotype	Significance	ClinVar
1-170532026-T-C			Benign (May 12, 2021)
1-170532148-GA-CT		Geroderma osteodysplastica	Pathogenic/Likely pathogenic (Dec 30, 2017)
1-170532151-G-A		Geroderma osteodysplastica	Uncertain significance (Apr 27, 2017)
1-170532153-G-T		Inborn genetic diseases • Geroderma osteodysplastica	Uncertain significance (Apr 11, 2023)
1-170532156-G-A			Pathogenic (Sep 27, 2023)
1-170532155-T-TGGGCAGCAGTGTTGGCAGTCGC			Pathogenic (Dec 17, 2022)
1-170532157-G-C			Uncertain significance (Apr 30, 2022)
1-170532159-C-A			Uncertain significance (Aug 09, 2022)
1-170532159-C-T			Uncertain significance (Aug 19, 2022)
1-170532160-A-G			Likely benign (Feb 20, 2022)
1-170532160-A-T			Likely benign (Oct 23, 2023)
1-170532162-C-T			Uncertain significance (Nov 01, 2021)
1-170532163-A-C			Likely benign (Jan 22, 2024)
1-170532163-A-G			Likely benign (Oct 04, 2023)
1-170532167-T-C		Geroderma osteodysplastica	Conflicting classifications of pathogenicity (Dec 14, 2023)
1-170532171-C-A		Geroderma osteodysplastica	Uncertain significance (Apr 11, 2023)
1-170532174-T-G			Uncertain significance (Aug 22, 2022)
1-170532175-C-T			Likely benign (Jan 20, 2024)
1-170532175-C-CG		Geroderma osteodysplastica • Inborn genetic diseases	Conflicting classifications of pathogenicity (Jan 25, 2024)
1-170532178-G-A			Likely benign (Jan 25, 2024)
1-170532178-G-T			Likely benign (Nov 15, 2023)
1-170532180-C-T		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
1-170532184-G-C			Likely benign (Jul 12, 2021)
1-170532185-A-G		Inborn genetic diseases	Uncertain significance (Feb 26, 2024)
1-170532186-G-T			Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GORAB	protein_coding	protein_coding	ENST00000367763	5	21318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000665	0.905	125704	0	42	125746	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.180	223	216	1.03	0.0000123	2575
Missense in Polyphen		64	71.77	0.89173		858
Synonymous	-1.08	91	78.8	1.16	0.00000429	751
Loss of Function	1.61	11	18.4	0.596	0.00000111	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000532	0.000532
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000159	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Geroderma osteodysplasticum (GO) [MIM:231070]: A rare autosomal recessive disorder characterized by lax, wrinkled skin, joint laxity and a typical face with a prematurely aged appearance. Skeletal signs include severe osteoporosis leading to frequent fractures, malar and mandibular hypoplasia and a variable degree of growth retardation. {ECO:0000269|PubMed:18997784}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: p53 signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0895

Intolerance Scores

• loftool: 0.887
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.393
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.239

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gorab
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype

Gene ontology

• Biological process: hair follicle morphogenesis;positive regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning;non-motile cilium assembly
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;Golgi apparatus;cytosol
• Molecular function: protein binding