PLEKHG4

pleckstrin homology and RhoGEF domain containing G4, the group of Pleckstrin homology domain containing|Dbl family Rho GEFs

Basic information

Region (hg38): 16:67277510-67289499

Previous symbols: [ "SCA4" ]

Links

ENSG00000196155 ∙ NCBI:25894 ∙ OMIM:609526 ∙ HGNC:24501 ∙ Uniprot:Q58EX7 ∙ 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 PLEKHG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHG4 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			68	5	2	75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	69	7	2

Variants in PLEKHG4

This is a list of pathogenic ClinVar variants found in the PLEKHG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67280029-C-T		Spinocerebellar ataxia type 31	Uncertain significance (Jan 01, 2007)
16-67280144-G-A		not specified	Uncertain significance (Jun 04, 2024)
16-67280150-G-A		not specified	Uncertain significance (Feb 05, 2024)
16-67280167-G-A		not specified	Uncertain significance (Dec 06, 2022)
16-67280171-G-A		not specified	Likely benign (Mar 13, 2023)
16-67280171-G-T		not specified	Uncertain significance (Dec 21, 2022)
16-67280204-G-A		not specified	Uncertain significance (Dec 06, 2022)
16-67280250-A-T		not specified	Uncertain significance (May 05, 2023)
16-67280306-G-A		not specified	Uncertain significance (Aug 01, 2022)
16-67280372-T-A		not specified	Uncertain significance (Jul 12, 2023)
16-67280532-T-C		not specified	Uncertain significance (Jun 21, 2022)
16-67280738-C-T		not specified	Uncertain significance (May 18, 2023)
16-67280887-C-T			Benign (Aug 01, 2024)
16-67280906-C-T		not specified	Uncertain significance (Jan 30, 2024)
16-67280924-C-T		not specified	Uncertain significance (Apr 12, 2022)
16-67280960-G-A		not specified	Uncertain significance (May 11, 2022)
16-67280974-C-T		not specified	Uncertain significance (Jun 21, 2022)
16-67280975-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-67281106-A-C			Likely benign (Nov 01, 2024)
16-67281107-C-T			Uncertain significance (May 01, 2016)
16-67281131-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-67281163-C-A		not specified	Uncertain significance (May 24, 2023)
16-67281630-C-G		not specified	Uncertain significance (Aug 17, 2021)
16-67281736-C-T		not specified	Likely benign (Aug 12, 2021)
16-67281767-C-A		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHG4	protein_coding	protein_coding	ENST00000360461	21	11990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.10e-16	0.998	125532	1	215	125748	0.000859

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	578	673	0.859	0.0000435	7591
Missense in Polyphen		132	164.13	0.80422		1941
Synonymous	0.953	273	294	0.929	0.0000182	2558
Loss of Function	3.06	36	62.0	0.580	0.00000375	615

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000855	0.000854
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.000382	0.000381
Finnish	0.000235	0.000231
European (Non-Finnish)	0.00121	0.00120
Middle Eastern	0.000382	0.000381
South Asian	0.00114	0.00111
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible role in intracellular signaling and cytoskeleton dynamics at the Golgi.

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.936
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.75

Haploinsufficiency Scores

• pHI: 0.201
• hipred: N
• hipred_score: 0.440
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.312

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhg4

Gene ontology

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