ARHGEF10L

Rho guanine nucleotide exchange factor 10 like, the group of Dbl family Rho GEFs

Basic information

Region (hg38): 1:17539697-17697874

Links

ENSG00000074964 ∙ NCBI:55160 ∙ OMIM:612494 ∙ HGNC:25540 ∙ Uniprot:Q9HCE6 ∙ 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 ARHGEF10L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARHGEF10L 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				3	3	6
missense		1	63	4	3	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	1	63	7	7

Variants in ARHGEF10L

This is a list of pathogenic ClinVar variants found in the ARHGEF10L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-17580621-A-G		not specified	Uncertain significance (May 04, 2023)
1-17587583-G-A		not specified	Uncertain significance (Apr 19, 2024)
1-17587597-A-G		not specified	Uncertain significance (Aug 04, 2023)
1-17587608-C-A		not specified	Uncertain significance (May 11, 2022)
1-17587636-C-T		not specified	Uncertain significance (Feb 08, 2023)
1-17588472-G-A		not specified	Likely benign (Dec 13, 2023)
1-17602159-C-A			Likely benign (Oct 01, 2022)
1-17602182-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-17602183-G-A			Benign (Mar 29, 2018)
1-17602212-C-T		not specified	Uncertain significance (May 03, 2023)
1-17602213-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-17603512-C-G		not specified	Uncertain significance (Mar 15, 2024)
1-17603513-C-T		not specified	Uncertain significance (May 14, 2024)
1-17607837-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-17607936-G-A		not specified	Uncertain significance (Mar 27, 2023)
1-17607948-G-A		not specified	Likely benign (Aug 15, 2023)
1-17613128-T-C		not specified	Uncertain significance (Aug 16, 2022)
1-17613131-G-A		not specified	Uncertain significance (Nov 29, 2023)
1-17613131-G-C		not specified	Uncertain significance (Apr 04, 2024)
1-17616097-A-G		not specified	Uncertain significance (Jan 03, 2022)
1-17616097-A-T		not specified	Uncertain significance (Jun 01, 2022)
1-17619374-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-17621893-C-T		not specified	Likely benign (May 20, 2024)
1-17622992-G-T			Benign (May 31, 2018)
1-17623054-A-T		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARHGEF10L	protein_coding	protein_coding	ENST00000361221	28	158040

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000473	1.00	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	672	791	0.849	0.0000507	8257
Missense in Polyphen		152	219.74	0.69172		2178
Synonymous	-0.370	351	342	1.03	0.0000240	2583
Loss of Function	5.06	18	60.4	0.298	0.00000286	678

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000355	0.000355
Ashkenazi Jewish	0.00	0.00
East Asian	0.000385	0.000381
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000129	0.000123
Middle Eastern	0.000385	0.000381
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RHOA, RHOB and RHOC. {ECO:0000269|PubMed:16112081}.
• 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)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.569
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.563
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arhgef10l

Gene ontology

• Biological process: actin cytoskeleton organization;SREBP signaling pathway;regulation of Rho protein signal transduction;positive regulation of GTPase activity;positive regulation of stress fiber assembly
• Cellular component: cytosol
• Molecular function: guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity