PLEKHG7

pleckstrin homology and RhoGEF domain containing G7, the group of Pleckstrin homology domain containing|Dbl family Rho GEFs

Basic information

Region (hg38): 12:92702843-92772455

Previous symbols: [ "C12orf74" ]

Links

ENSG00000187510 ∙ NCBI:440107 ∙ ∙ HGNC:33829 ∙ Uniprot:Q6ZR37 ∙ 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 PLEKHG7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHG7 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	1	2
missense			24	1	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	2

Variants in PLEKHG7

This is a list of pathogenic ClinVar variants found in the PLEKHG7 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-92706717-A-G			Benign (Jul 23, 2018)
12-92706817-G-A			Benign (Jul 23, 2018)
12-92740884-C-T		not specified	Uncertain significance (Jul 08, 2022)
12-92741540-T-C		not specified	Uncertain significance (Jul 14, 2021)
12-92741581-G-A		not specified	Uncertain significance (Aug 15, 2023)
12-92745479-A-G		not specified	Uncertain significance (May 30, 2024)
12-92745575-T-G		not specified	Uncertain significance (Mar 07, 2025)
12-92754108-C-A		not specified	Uncertain significance (Apr 06, 2024)
12-92754109-A-C		not specified	Uncertain significance (Aug 02, 2021)
12-92754126-G-T		not specified	Likely benign (Jan 16, 2025)
12-92754154-A-G		not specified	Uncertain significance (Aug 20, 2024)
12-92754217-A-G		not specified	Uncertain significance (Jun 22, 2023)
12-92754228-A-G		not specified	Uncertain significance (Apr 20, 2024)
12-92755836-G-A		not specified	Uncertain significance (Feb 21, 2024)
12-92755912-A-C		not specified	Uncertain significance (Jan 17, 2025)
12-92755925-G-T		not specified	Uncertain significance (Aug 14, 2024)
12-92756321-A-G			Likely benign (Dec 01, 2022)
12-92756328-G-A		not specified	Uncertain significance (Aug 21, 2023)
12-92761764-T-G		not specified	Uncertain significance (Mar 25, 2024)
12-92761781-T-G		not specified	Uncertain significance (Jan 19, 2025)
12-92761790-A-G		not specified	Likely benign (Jan 03, 2024)
12-92764056-G-C		not specified	Uncertain significance (Dec 20, 2023)
12-92764070-G-A		not specified	Uncertain significance (Oct 12, 2022)
12-92764075-C-T		not specified	Uncertain significance (Aug 01, 2024)
12-92764134-G-A		not specified	Uncertain significance (Jul 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHG7	protein_coding	protein_coding	ENST00000344636	11	50951

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.89e-19	0.000892	125453	1	286	125740	0.00114

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.248	183	193	0.950	0.00000954	2480
Missense in Polyphen		28	33.132	0.84511		463
Synonymous	1.06	61	72.5	0.841	0.00000396	689
Loss of Function	-0.546	27	24.1	1.12	0.00000133	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00970	0.00967
Ashkenazi Jewish	0.00	0.00
East Asian	0.000669	0.000653
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000497	0.000422
Middle Eastern	0.000669	0.000653
South Asian	0.00190	0.00180
Other	0.00132	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.929
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.212
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0567

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of Rho protein signal transduction
• Molecular function: Rho guanyl-nucleotide exchange factor activity