PLEKHG4B

pleckstrin homology and RhoGEF domain containing G4B, the group of Dbl family Rho GEFs|Pleckstrin homology domain containing

Basic information

Region (hg38): 5:92168-189972

Links

ENSG00000153404 ∙ NCBI:153478 ∙ ∙ HGNC:29399 ∙ Uniprot:Q96PX9 ∙ 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 PLEKHG4B gene.

• not_specified (269 variants)
• not_provided (7 variants)
• Abnormality_of_neuronal_migration (2 variants)
• Prostate_cancer (1 variants)
• Neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHG4B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000052909.5. 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	2	2	5
missense			249	26	2	277
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	252	28	4

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHG4B	protein_coding	protein_coding	ENST00000283426	18	49713

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-32	0.0000497	125612	1	135	125748	0.000541

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.271	762	741	1.03	0.0000466	8151
Missense in Polyphen		186	203.28	0.915		2422
Synonymous	-0.602	332	318	1.04	0.0000210	2620
Loss of Function	0.221	50	51.7	0.967	0.00000289	551

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00100
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000393	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000397	0.000387
Middle Eastern	0.000393	0.000381
South Asian	0.00168	0.00163
Other	0.000667	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.609
• rvis_EVS: -0.1
• rvis_percentile_EVS: 45.61

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.144
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

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