PLEKHG1

pleckstrin homology and RhoGEF domain containing G1, the group of Dbl family Rho GEFs|Pleckstrin homology domain containing

Basic information

Region (hg38): 6:150599882-150843665

Links

ENSG00000120278 ∙ NCBI:57480 ∙ OMIM:620134 ∙ HGNC:20884 ∙ Uniprot:Q9ULL1 ∙ 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 PLEKHG1 gene.

• Inborn genetic diseases (58 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHG1 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
missense			57	1		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	2	0

Variants in PLEKHG1

This is a list of pathogenic ClinVar variants found in the PLEKHG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-150733694-G-A		not specified	Uncertain significance (Aug 22, 2023)
6-150733701-A-C		not specified	Uncertain significance (Feb 28, 2023)
6-150733766-G-A		not specified	Uncertain significance (Feb 21, 2024)
6-150733830-G-A		not specified	Uncertain significance (Dec 08, 2023)
6-150733902-C-T		not specified	Uncertain significance (Oct 29, 2021)
6-150733932-A-G		not specified	Uncertain significance (Jan 31, 2022)
6-150733970-G-A		not specified	Uncertain significance (Sep 22, 2021)
6-150733977-C-G		not specified	Uncertain significance (Dec 02, 2021)
6-150733983-C-A		not specified	Uncertain significance (Sep 01, 2021)
6-150733983-C-T		not specified	Uncertain significance (Feb 05, 2024)
6-150734058-G-A		not specified	Uncertain significance (Dec 07, 2021)
6-150768659-G-A		not specified	Uncertain significance (Apr 12, 2022)
6-150768722-A-G		not specified	Uncertain significance (Mar 06, 2023)
6-150768726-A-G		not specified	Uncertain significance (Aug 12, 2022)
6-150795863-A-C		not specified	Uncertain significance (Oct 31, 2023)
6-150800723-G-A		not specified	Uncertain significance (Jan 27, 2022)
6-150800780-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-150809193-G-A		not specified	Uncertain significance (Jan 04, 2022)
6-150819714-A-G		not specified	Uncertain significance (Sep 17, 2021)
6-150830601-C-A		not specified	Uncertain significance (Oct 27, 2023)
6-150830672-A-G		not specified	Uncertain significance (Oct 06, 2022)
6-150830675-G-A		not specified	Uncertain significance (Sep 16, 2021)
6-150830733-C-T		not specified	Uncertain significance (Jul 11, 2023)
6-150830736-T-G		not specified	Uncertain significance (Jun 07, 2023)
6-150830941-C-A		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHG1	protein_coding	protein_coding	ENST00000367328	15	243801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0127	0.987	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.616	733	781	0.938	0.0000451	9160
Missense in Polyphen		171	195.76	0.87353		2330
Synonymous	-1.11	343	318	1.08	0.0000199	2672
Loss of Function	5.08	15	56.1	0.268	0.00000290	675

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000457	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000601	0.000601
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.631
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.93

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.443
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhg1
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of Rho protein signal transduction
• Cellular component: nucleus;nucleoplasm
• Molecular function: Rho guanyl-nucleotide exchange factor activity