ARFGEF3

ARFGEF family member 3, the group of Protein phosphatase 1 regulatory subunits|ARFGEF family|Armadillo like helical domain containing

Basic information

Region (hg38): 6:138161939-138344663

Previous symbols: [ "C6orf92", "KIAA1244" ]

Links

ENSG00000112379NCBI:57221OMIM:617411HGNC:21213Uniprot:Q5TH69AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARFGEF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARFGEF3 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
17
clinvar
14
clinvar
31
missense
102
clinvar
9
clinvar
8
clinvar
119
nonsense
2
clinvar
2
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
1
3
5
9
non coding
6
clinvar
1
clinvar
2
clinvar
9
Total 0 0 110 28 24

Variants in ARFGEF3

This is a list of pathogenic ClinVar variants found in the ARFGEF3 region.

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

Position Type Phenotype Significance ClinVar
6-138170717-G-A ARFGEF3-related disorder Benign (Jan 02, 2020)3041335
6-138207094-C-G not specified Uncertain significance (Sep 17, 2021)2251340
6-138207098-C-G not specified Uncertain significance (Oct 27, 2021)2257750
6-138209955-G-T ARFGEF3-related disorder Likely benign (Feb 08, 2023)3035248
6-138210011-C-T Benign (Sep 11, 2018)715845
6-138210014-C-A not specified Uncertain significance (Apr 07, 2023)2521052
6-138210014-C-T Likely benign (May 24, 2018)744372
6-138218163-T-A not specified Uncertain significance (Jan 07, 2022)2271073
6-138218163-T-C not specified Uncertain significance (Feb 28, 2023)2457522
6-138218221-C-T not specified Uncertain significance (Jul 11, 2023)2590740
6-138218226-T-C not specified Uncertain significance (Oct 12, 2022)2318401
6-138218253-A-G not specified Uncertain significance (Mar 14, 2023)3209020
6-138218278-C-T not specified Uncertain significance (Aug 28, 2023)2621904
6-138218303-G-A Likely benign (Jun 01, 2022)2656937
6-138238516-T-C not specified Uncertain significance (Feb 28, 2024)3128402
6-138242953-T-A not specified Uncertain significance (Jun 21, 2022)2295655
6-138245582-C-T ARFGEF3-related disorder Benign (Jul 22, 2019)3049634
6-138245583-C-T ARFGEF3-related disorder Likely benign (Feb 21, 2019)3035094
6-138253899-C-T not specified Uncertain significance (Dec 02, 2022)2344775
6-138253951-T-C ARFGEF3-related disorder Likely benign (Jun 17, 2019)3034386
6-138253955-C-A not specified Uncertain significance (Jul 26, 2022)2303238
6-138253962-A-T not specified Uncertain significance (Nov 22, 2022)2222808
6-138253966-G-A not specified Uncertain significance (Jan 23, 2024)3128413
6-138255522-G-A not specified Uncertain significance (Jan 02, 2024)3128414
6-138255545-G-A not specified Uncertain significance (May 21, 2024)3310295

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ARFGEF3protein_codingprotein_codingENST00000251691 34182743
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.001.87e-71255640291255930.000115
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.509841.23e+30.7990.000073114155
Missense in Polyphen310444.440.697515096
Synonymous1.374865260.9240.00003564305
Loss of Function7.941295.90.1250.000005021100

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002830.000271
Ashkenazi Jewish0.0001990.000199
East Asian0.0001630.000163
Finnish0.00004730.0000462
European (Non-Finnish)0.00007280.0000705
Middle Eastern0.0001630.000163
South Asian0.0002970.000294
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Participates in the regulation of systemic glucose homeostasis, where it negatively regulates insulin granule biogenesis in pancreatic islet beta cells (By similarity). Also regulates glucagon granule production in pancreatic alpha cells (By similarity). Inhibits nuclear translocation of the transcriptional coregulator PHB2 and may enhance estrogen receptor alpha (ESR1) transcriptional activity in breast cancer cells (PubMed:19496786). {ECO:0000250|UniProtKB:Q3UGY8, ECO:0000269|PubMed:19496786}.;

Recessive Scores

pRec
0.125

Intolerance Scores

loftool
rvis_EVS
-2.22
rvis_percentile_EVS
1.34

Haploinsufficiency Scores

pHI
hipred
Y
hipred_score
0.646
ghis
0.587

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Arfgef3
Phenotype
cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process
negative regulation of phosphatase activity;regulation of ARF protein signal transduction
Cellular component
integral component of membrane;transport vesicle membrane
Molecular function
ARF guanyl-nucleotide exchange factor activity