RAP1GDS1

Rap1 GTPase-GDP dissociation stimulator 1, the group of Armadillo repeat containing

Basic information

Region (hg38): 4:98261384-98443858

Links

ENSG00000138698 ∙ NCBI:5910 ∙ OMIM:179502 ∙ HGNC:9859 ∙ Uniprot:P52306 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Alfadhel syndrome	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	Craniofacial; Musculoskeletal; Neurologic	32431071; 33875846

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAP1GDS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAP1GDS1 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	1	2
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	30	2	1

Variants in RAP1GDS1

This is a list of pathogenic ClinVar variants found in the RAP1GDS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-98293481-CT-C		Alfadhel syndrome	Pathogenic (Dec 18, 2023)
4-98343141-A-G		not specified	Uncertain significance (Apr 05, 2023)
4-98343186-T-C		not specified	Uncertain significance (Apr 27, 2023)
4-98343189-G-T		not specified	Uncertain significance (Jul 11, 2023)
4-98343193-G-A		not specified	Uncertain significance (Mar 16, 2022)
4-98352481-A-G		not specified	Uncertain significance (Mar 25, 2024)
4-98352484-C-A			Benign (May 24, 2018)
4-98352553-G-A			Likely benign (Dec 01, 2022)
4-98352590-G-A			Uncertain significance (Apr 18, 2022)
4-98379107-A-G		not specified	Uncertain significance (Dec 09, 2023)
4-98379115-C-T		not specified	Uncertain significance (Jan 11, 2023)
4-98379116-T-C		not specified	Uncertain significance (Mar 23, 2022)
4-98391954-T-G		not specified	Uncertain significance (Jan 23, 2024)
4-98391976-A-G		not specified	Uncertain significance (Oct 27, 2022)
4-98391984-G-A		not specified	Uncertain significance (Feb 05, 2024)
4-98404546-T-C		not specified	Uncertain significance (Jun 30, 2023)
4-98404549-A-G		not specified	Uncertain significance (May 17, 2023)
4-98404568-G-T		not specified	Uncertain significance (Apr 03, 2023)
4-98416805-A-T		not specified	Uncertain significance (Nov 10, 2022)
4-98416843-G-C		not specified	Uncertain significance (Feb 13, 2024)
4-98416878-A-C		not specified	Uncertain significance (Dec 21, 2022)
4-98417477-A-G		not specified	Uncertain significance (Jan 18, 2023)
4-98417499-G-A			Uncertain significance (Jan 28, 2024)
4-98418761-C-T		RAP1GDS1-related disorder	Likely benign (May 15, 2019)
4-98418775-A-C			Uncertain significance (Jun 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAP1GDS1	protein_coding	protein_coding	ENST00000339360	15	182478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.933	0.0671	124767	0	27	124794	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	252	305	0.827	0.0000141	3998
Missense in Polyphen		58	84.46	0.68671		1156
Synonymous	0.929	95	107	0.886	0.00000506	1161
Loss of Function	4.29	5	30.6	0.163	0.00000157	388

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.00	0.00
Finnish	0.000186	0.000186
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000327
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulates GDP/GTP exchange reaction of a group of small GTP-binding proteins (G proteins) including Rap1a/Rap1b, RhoA, RhoB and KRas, by stimulating the dissociation of GDP from and the subsequent binding of GTP to each small G protein.
• Pathway: Regulation of RAC1 activity (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.825
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.233
• hipred: Y
• hipred_score: 0.822
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.640

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rap1gds1

Gene ontology

• Biological process: vascular smooth muscle contraction;myosin filament assembly;negative regulation of endoplasmic reticulum calcium ion concentration;positive regulation of GTPase activity;positive regulation of mitochondrial calcium ion concentration
• Cellular component: mitochondrion;endoplasmic reticulum;cytosol;extracellular exosome
• Molecular function: GTPase activator activity;protein binding