PLEKHG3

pleckstrin homology and RhoGEF domain containing G3, the group of Pleckstrin homology domain containing|Dbl family Rho GEFs

Basic information

Region (hg38): 14:64704102-64750249

Previous symbols: [ "KIAA0599" ]

Links

ENSG00000126822 ∙ NCBI:26030 ∙ OMIM:617940 ∙ HGNC:20364 ∙ Uniprot:A1L390 ∙ 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 PLEKHG3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHG3 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				8	2	10
missense			93	9	7	109
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding			13	2	3	18
Total	0	0	107	19	12

Variants in PLEKHG3

This is a list of pathogenic ClinVar variants found in the PLEKHG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-64727635-C-G		not specified	Uncertain significance (Dec 07, 2021)
14-64727659-G-T		not specified	Uncertain significance (Sep 06, 2022)
14-64727674-C-T		not specified	Uncertain significance (Nov 15, 2021)
14-64727708-C-T		not specified	Uncertain significance (Mar 24, 2023)
14-64727710-G-C		not specified	Uncertain significance (Mar 04, 2024)
14-64727714-C-T		not specified	Uncertain significance (Jan 23, 2023)
14-64727798-G-A		not specified	Uncertain significance (May 02, 2024)
14-64727818-A-G		not specified	Uncertain significance (May 15, 2024)
14-64727828-G-A		not specified	Uncertain significance (Mar 15, 2024)
14-64727832-C-G		not specified	Uncertain significance (Nov 07, 2022)
14-64727842-G-A		not specified	Likely benign (Sep 26, 2022)
14-64727872-C-T		not specified	Uncertain significance (Apr 28, 2022)
14-64727904-C-T			Likely benign (Feb 01, 2023)
14-64727906-G-A		not specified	Uncertain significance (Aug 11, 2022)
14-64727977-G-A		not specified	Uncertain significance (Dec 26, 2023)
14-64727991-C-T			Benign (Dec 28, 2017)
14-64730252-C-T			Likely benign (Dec 31, 2019)
14-64730816-C-T			Benign (Sep 10, 2018)
14-64730827-C-T		not specified	Uncertain significance (Nov 15, 2021)
14-64730920-C-T		not specified	Uncertain significance (Sep 22, 2022)
14-64731080-G-T		not specified	Uncertain significance (Aug 28, 2023)
14-64731175-C-G			Likely benign (Oct 02, 2018)
14-64731412-G-A		not specified	Uncertain significance (Dec 28, 2022)
14-64731439-C-T			Benign (Sep 10, 2018)
14-64731442-G-A		not specified	Uncertain significance (Sep 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHG3	protein_coding	protein_coding	ENST00000247226	14	42791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.68e-8	1.00	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.435	698	731	0.955	0.0000469	7555
Missense in Polyphen		189	212.02	0.89144		2194
Synonymous	0.906	283	303	0.934	0.0000193	2396
Loss of Function	3.41	20	44.6	0.448	0.00000231	501

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000436	0.000424
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000219	0.000217
Finnish	0.0000985	0.0000924
European (Non-Finnish)	0.000217	0.000202
Middle Eastern	0.000219	0.000217
South Asian	0.000139	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0913

Intolerance Scores

• loftool: 0.370
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.29

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.229
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhg3
• Phenotype: vision/eye phenotype

Gene ontology

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