PLEKHH3

pleckstrin homology, MyTH4 and FERM domain containing H3, the group of FERM domain containing|Pleckstrin homology domain containing

Basic information

Region (hg38): 17:42667914-42676994

Links

ENSG00000068137 ∙ NCBI:79990 ∙ ∙ HGNC:26105 ∙ Uniprot:Q7Z736 ∙ 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 PLEKHH3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHH3 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				2		2
missense			89	2	1	92
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	89	4	1

Variants in PLEKHH3

This is a list of pathogenic ClinVar variants found in the PLEKHH3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42668141-G-T		not specified	Uncertain significance (Jan 07, 2025)
17-42668171-C-T		not specified	Uncertain significance (Aug 20, 2024)
17-42668172-G-T		not specified	Uncertain significance (May 15, 2024)
17-42668180-C-T		not specified	Uncertain significance (Jan 29, 2024)
17-42668185-C-T		not specified	Likely benign (Nov 08, 2021)
17-42668197-G-A		not specified	Uncertain significance (May 20, 2024)
17-42668228-G-A		not specified	Uncertain significance (Feb 20, 2025)
17-42668230-G-C		not specified	Uncertain significance (Oct 10, 2023)
17-42668252-C-T		not specified	Uncertain significance (Jun 22, 2023)
17-42668297-C-T		not specified	Uncertain significance (May 16, 2024)
17-42669521-C-T		not specified	Uncertain significance (Jul 07, 2022)
17-42669944-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-42669949-G-A		not specified	Uncertain significance (Jan 24, 2024)
17-42669953-C-T		not specified	Uncertain significance (Nov 13, 2023)
17-42669970-G-A		not specified	Uncertain significance (Feb 08, 2025)
17-42669976-A-G		not specified	Uncertain significance (Oct 12, 2024)
17-42669997-G-C		not specified	Uncertain significance (Oct 14, 2023)
17-42670000-T-C		not specified	Uncertain significance (Oct 14, 2023)
17-42670031-A-C		not specified	Uncertain significance (Jun 10, 2022)
17-42670034-C-A		not specified	Uncertain significance (Apr 19, 2024)
17-42670049-C-G		not specified	Uncertain significance (Jan 09, 2025)
17-42670054-G-A		not specified	Uncertain significance (Aug 14, 2023)
17-42670055-T-G		not specified	Uncertain significance (Sep 17, 2021)
17-42670061-C-T		not specified	Uncertain significance (May 28, 2023)
17-42670087-C-T		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHH3	protein_coding	protein_coding	ENST00000591022	13	9117

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.84e-7	0.998	125673	0	64	125737	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	344	444	0.774	0.0000296	4851
Missense in Polyphen		36	49.101	0.73319		557
Synonymous	2.24	171	213	0.805	0.0000142	1818
Loss of Function	2.77	16	33.2	0.482	0.00000182	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000183
Ashkenazi Jewish	0.000129	0.0000992
East Asian	0.0000547	0.0000544
Finnish	0.00191	0.00190
European (Non-Finnish)	0.000130	0.000114
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0968

Intolerance Scores

• loftool: 0.223
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.17

Haploinsufficiency Scores

• pHI: 0.576
• hipred: Y
• hipred_score: 0.563
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhh3

Gene ontology

• Biological process: signal transduction
• Cellular component: extracellular space;cytoskeleton