ARFGEF3
Basic information
Region (hg38): 6:138161939-138344663
Previous symbols: [ "C6orf92", "KIAA1244" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 14 | 31 | |||
missense | 102 | 119 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 3 | 5 | 9 | ||
non coding | 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) | ||
6-138207094-C-G | not specified | Uncertain significance (Sep 17, 2021) | ||
6-138207098-C-G | not specified | Uncertain significance (Oct 27, 2021) | ||
6-138209955-G-T | ARFGEF3-related disorder | Likely benign (Feb 08, 2023) | ||
6-138210011-C-T | Benign (Sep 11, 2018) | |||
6-138210014-C-A | not specified | Uncertain significance (Apr 07, 2023) | ||
6-138210014-C-T | Likely benign (May 24, 2018) | |||
6-138218163-T-A | not specified | Uncertain significance (Jan 07, 2022) | ||
6-138218163-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
6-138218221-C-T | not specified | Uncertain significance (Jul 11, 2023) | ||
6-138218226-T-C | not specified | Uncertain significance (Oct 12, 2022) | ||
6-138218253-A-G | not specified | Uncertain significance (Mar 14, 2023) | ||
6-138218278-C-T | not specified | Uncertain significance (Aug 28, 2023) | ||
6-138218303-G-A | Likely benign (Jun 01, 2022) | |||
6-138238516-T-C | not specified | Uncertain significance (Feb 28, 2024) | ||
6-138242953-T-A | not specified | Uncertain significance (Jun 21, 2022) | ||
6-138245582-C-T | ARFGEF3-related disorder | Benign (Jul 22, 2019) | ||
6-138245583-C-T | ARFGEF3-related disorder | Likely benign (Feb 21, 2019) | ||
6-138253899-C-T | not specified | Uncertain significance (Dec 02, 2022) | ||
6-138253951-T-C | ARFGEF3-related disorder | Likely benign (Jun 17, 2019) | ||
6-138253955-C-A | not specified | Uncertain significance (Jul 26, 2022) | ||
6-138253962-A-T | not specified | Uncertain significance (Nov 22, 2022) | ||
6-138253966-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
6-138255522-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
6-138255545-G-A | not specified | Uncertain significance (May 21, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ARFGEF3 | protein_coding | protein_coding | ENST00000251691 | 34 | 182743 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 1.87e-7 | 125564 | 0 | 29 | 125593 | 0.000115 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.50 | 984 | 1.23e+3 | 0.799 | 0.0000731 | 14155 |
Missense in Polyphen | 310 | 444.44 | 0.69751 | 5096 | ||
Synonymous | 1.37 | 486 | 526 | 0.924 | 0.0000356 | 4305 |
Loss of Function | 7.94 | 12 | 95.9 | 0.125 | 0.00000502 | 1100 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000283 | 0.000271 |
Ashkenazi Jewish | 0.000199 | 0.000199 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.0000473 | 0.0000462 |
European (Non-Finnish) | 0.0000728 | 0.0000705 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.000297 | 0.000294 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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