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.

• not_specified (123 variants)
• not_provided (5 variants)

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. These statistics are base on transcript: NM_000024927.5. 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				2		2
missense			122	2	1	125
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	122	4	1

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