RAPGEF6

Rap guanine nucleotide exchange factor 6, the group of PDZ domain containing

Basic information

Region (hg38): 5:131423921-131635231

Previous symbols: [ "PDZGEF2" ]

Links

ENSG00000158987 ∙ NCBI:51735 ∙ OMIM:610499 ∙ HGNC:20655 ∙ Uniprot:Q8TEU7 ∙ 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 RAPGEF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAPGEF6 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	3	4
missense			81	1	1	83
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	81	2	5

Variants in RAPGEF6

This is a list of pathogenic ClinVar variants found in the RAPGEF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-131427271-C-G		not specified	Uncertain significance (Oct 31, 2023)
5-131429003-G-A		not specified	Uncertain significance (Aug 16, 2021)
5-131429006-A-T			Benign (Jul 17, 2018)
5-131429043-A-G		not specified	Uncertain significance (Aug 12, 2021)
5-131429063-T-A		not specified	Uncertain significance (Jul 26, 2022)
5-131429105-T-A		not specified	Uncertain significance (Apr 04, 2023)
5-131429132-G-A		not specified	Uncertain significance (Jun 26, 2024)
5-131429184-T-C		not specified	Uncertain significance (Apr 09, 2024)
5-131429187-C-T		not specified	Uncertain significance (Jun 07, 2023)
5-131430849-C-A			Benign (Dec 31, 2019)
5-131430929-G-T			Benign (Jul 13, 2018)
5-131430946-C-G		not specified	Uncertain significance (Oct 26, 2024)
5-131431028-A-C		not specified	Uncertain significance (Mar 31, 2024)
5-131431044-C-T		not specified	Uncertain significance (May 29, 2024)
5-131431122-G-A		not specified	Uncertain significance (Dec 13, 2021)
5-131431160-C-A		not specified	Uncertain significance (Jul 09, 2024)
5-131431212-C-T		not specified	Uncertain significance (Jun 06, 2023)
5-131431251-G-A		not specified	Uncertain significance (Feb 17, 2024)
5-131431345-T-C		not specified	Uncertain significance (Jul 18, 2024)
5-131433449-G-C		not specified	Uncertain significance (Mar 24, 2023)
5-131433466-G-A		not specified	Uncertain significance (Nov 30, 2021)
5-131433542-G-C		not specified	Uncertain significance (Sep 27, 2021)
5-131433600-C-G		not specified	Uncertain significance (Mar 20, 2024)
5-131433658-C-T		not specified	Uncertain significance (Sep 22, 2023)
5-131439670-C-T		not specified	Uncertain significance (May 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAPGEF6	protein_coding	protein_coding	ENST00000296859	29	211316

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00356	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	723	851	0.850	0.0000428	10665
Missense in Polyphen		302	417.88	0.7227		5281
Synonymous	-0.763	313	296	1.06	0.0000150	3000
Loss of Function	6.74	14	78.3	0.179	0.00000409	989

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000629	0.000626
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) for Rap1A, Rap2A and M-Ras GTPases. Does not interact with cAMP. {ECO:0000269|PubMed:11524421, ECO:0000269|PubMed:12581858}.
• Pathway: Tight junction - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• loftool: 0.778
• rvis_EVS: -1.67
• rvis_percentile_EVS: 2.7

Haploinsufficiency Scores

• pHI: 0.690
• hipred: N
• hipred_score: 0.466
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.853

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rapgef6
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; hematopoietic system phenotype; reproductive system phenotype; immune system phenotype

Gene ontology

• Biological process: Ras protein signal transduction;microvillus assembly;regulation of GTPase activity;positive regulation of GTPase activity;protein localization to plasma membrane;establishment of endothelial intestinal barrier
• Cellular component: centrosome;cytosol;plasma membrane;apical plasma membrane;endocytic vesicle
• Molecular function: guanyl-nucleotide exchange factor activity;protein binding;Ras GTPase binding;GTP-dependent protein binding;phosphatidic acid binding