PLEKHH1

pleckstrin homology, MyTH4 and FERM domain containing H1, the group of Pleckstrin homology domain containing|FERM domain containing

Basic information

Region (hg38): 14:67533289-67589612

Links

ENSG00000054690 ∙ NCBI:57475 ∙ ∙ HGNC:17733 ∙ Uniprot:Q9ULM0 ∙ 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 PLEKHH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHH1 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
missense			81	5		86
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	81	6	1

Variants in PLEKHH1

This is a list of pathogenic ClinVar variants found in the PLEKHH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-67541875-A-T		not specified	Uncertain significance (Feb 23, 2023)
14-67541901-G-A		not specified	Uncertain significance (May 26, 2024)
14-67541940-C-T		not specified	Uncertain significance (Dec 01, 2022)
14-67557338-C-T		not specified	Uncertain significance (May 01, 2022)
14-67557365-A-G		not specified	Uncertain significance (May 29, 2024)
14-67557371-G-A		not specified	Uncertain significance (Aug 08, 2023)
14-67557371-G-C		not specified	Uncertain significance (Feb 28, 2024)
14-67557394-G-C		not specified	Uncertain significance (Jun 10, 2024)
14-67559613-G-T		not specified	Uncertain significance (May 29, 2024)
14-67559686-G-A		not specified	Uncertain significance (Aug 20, 2023)
14-67561994-G-A		not specified	Likely benign (Apr 24, 2024)
14-67562155-C-T		not specified	Uncertain significance (Mar 28, 2024)
14-67562157-C-T		not specified	Uncertain significance (Jun 11, 2024)
14-67562173-C-T		not specified	Uncertain significance (Oct 12, 2022)
14-67562179-A-G		not specified	Uncertain significance (Jul 19, 2023)
14-67562184-G-A		not specified	Likely benign (May 24, 2024)
14-67562185-C-A		not specified	Uncertain significance (Jan 29, 2024)
14-67562196-G-A		not specified	Uncertain significance (Jun 17, 2024)
14-67562227-C-T		not specified	Uncertain significance (Jan 18, 2023)
14-67562230-T-C		not specified	Likely benign (Dec 28, 2023)
14-67562247-T-A		not specified	Uncertain significance (Dec 19, 2023)
14-67562370-G-A		not specified	Uncertain significance (May 26, 2023)
14-67562415-G-C		not specified	Uncertain significance (Jan 04, 2022)
14-67562445-C-A		not specified	Uncertain significance (Feb 07, 2023)
14-67562458-G-A		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHH1	protein_coding	protein_coding	ENST00000329153	28	56312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.68e-9	1.00	124538	0	142	124680	0.000570

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	611	763	0.800	0.0000437	8744
Missense in Polyphen		116	161.26	0.71934		1854
Synonymous	1.41	277	309	0.898	0.0000179	2752
Loss of Function	4.71	27	69.3	0.390	0.00000351	794

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00116
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000847	0.000835
Finnish	0.000749	0.000743
European (Non-Finnish)	0.000520	0.000504
Middle Eastern	0.000847	0.000835
South Asian	0.000567	0.000523
Other	0.000829	0.000825

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0838

Intolerance Scores

• loftool: 0.797
• rvis_EVS: 1.26
• rvis_percentile_EVS: 93.49

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.495
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhh1

Gene ontology

• Cellular component: cytoskeleton