ARHGEF10
Basic information
Region (hg38): 8:1823926-1958641
Links
Phenotypes
GenCC
Source:
- autosomal dominant slowed nerve conduction velocity (Supportive), mode of inheritance: AD
- peripheral neuropathy (Limited), mode of inheritance: AD
- autosomal dominant slowed nerve conduction velocity (Limited), mode of inheritance: Unknown
- autosomal dominant slowed nerve conduction velocity (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Slowed nerve conduction velocity, autosomal dominant (Hereditary motor and sensory neuropathy) | AD | 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 | Neurologic | 9678704; 14508709 |
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 ARHGEF10 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 | 108 | 25 | 138 | |||
missense | 363 | 20 | 11 | 394 | ||
nonsense | 10 | 10 | ||||
start loss | 0 | |||||
frameshift | 6 | |||||
inframe indel | 4 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
splice region | 17 | 17 | 10 | 44 | ||
non coding | 16 | 60 | 86 | 162 | ||
Total | 0 | 0 | 407 | 188 | 122 |
Variants in ARHGEF10
This is a list of pathogenic ClinVar variants found in the ARHGEF10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
8-1843267-C-T | Benign (May 10, 2021) | |||
8-1843424-C-A | Uncertain significance (Jul 22, 2022) | |||
8-1843441-C-T | ARHGEF10-related disorder | Likely benign (Mar 28, 2019) | ||
8-1843472-T-G | Benign (May 10, 2021) | |||
8-1843496-C-T | Benign (May 11, 2021) | |||
8-1843497-G-A | Benign (May 10, 2021) | |||
8-1843506-C-T | Benign (May 10, 2021) | |||
8-1843519-A-G | Benign (May 10, 2021) | |||
8-1857814-T-C | Benign (May 10, 2021) | |||
8-1857870-AGATC-A | Benign (May 10, 2021) | |||
8-1857875-GATCGATCT-G | Benign (May 11, 2021) | |||
8-1857875-GATCGATCTATCT-G | Benign (May 21, 2021) | |||
8-1857875-G-GATCT | Benign (May 10, 2021) | |||
8-1857879-G-T | Benign (May 10, 2021) | |||
8-1857879-GATCT-G | Benign (May 19, 2021) | |||
8-1857879-G-GATCT | Benign (May 10, 2021) | |||
8-1857947-TTTTTC-T | ARHGEF10-related disorder | Benign (Jan 24, 2024) | ||
8-1857950-T-C | Autosomal dominant slowed nerve conduction velocity • not specified | Benign/Likely benign (Jan 21, 2024) | ||
8-1857951-T-A | Likely benign (Oct 30, 2023) | |||
8-1857972-A-G | Uncertain significance (Jan 15, 2024) | |||
8-1857974-TATG-T | Uncertain significance (Jan 07, 2025) | |||
8-1857977-G-T | Uncertain significance (Jul 26, 2022) | |||
8-1857995-G-C | Uncertain significance (Jul 17, 2024) | |||
8-1857996-A-G | Uncertain significance (Oct 03, 2023) | |||
8-1857998-G-C | not specified | Uncertain significance (Sep 23, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ARHGEF10 | protein_coding | protein_coding | ENST00000349830 | 28 | 134666 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
6.77e-30 | 0.0301 | 125611 | 0 | 137 | 125748 | 0.000545 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -2.72 | 1013 | 797 | 1.27 | 0.0000515 | 8822 |
Missense in Polyphen | 355 | 327.32 | 1.0846 | 3595 | ||
Synonymous | -5.54 | 471 | 341 | 1.38 | 0.0000270 | 2598 |
Loss of Function | 1.72 | 54 | 69.4 | 0.778 | 0.00000369 | 808 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00107 | 0.00107 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000381 | 0.000381 |
Finnish | 0.000603 | 0.000601 |
European (Non-Finnish) | 0.000555 | 0.000554 |
Middle Eastern | 0.000381 | 0.000381 |
South Asian | 0.000753 | 0.000752 |
Other | 0.000489 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role in developmental myelination of peripheral nerves. {ECO:0000269|PubMed:14508709}.;
- Disease
- DISEASE: Slowed nerve conduction velocity (SNCV) [MIM:608236]: Affected individuals present a reduction in nerve conduction velocities without any clinical signs of peripheral or central nervous system dysfunction. SNCV inheritance is autosomal dominant. {ECO:0000269|PubMed:14508709}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity
(Consensus)
Intolerance Scores
- loftool
- 0.799
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 8.11
Haploinsufficiency Scores
- pHI
- 0.220
- hipred
- Y
- hipred_score
- 0.540
- ghis
- 0.542
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.657
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arhgef10
- Phenotype
Gene ontology
- Biological process
- myelination in peripheral nervous system;actin cytoskeleton organization;regulation of Rho protein signal transduction;centrosome duplication;positive regulation of stress fiber assembly;mitotic spindle assembly;activation of GTPase activity
- Cellular component
- centrosome;cytosol
- Molecular function
- guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;protein binding;kinesin binding