PLEKHG1

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

Basic information

Region (hg38): 6:150599883-150843665

Links

ENSG00000120278 ∙ NCBI:57480 ∙ OMIM:620134 ∙ HGNC:20884 ∙ Uniprot:Q9ULL1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• periventricular leukomalacia (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLEKHG1 gene.

• not_specified (176 variants)
• not_provided (1 variants)
• Prostate_cancer (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. These statistics are base on transcript: NM_001029884.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			171	6		177
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	171	7	0

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