PLEKHD1

pleckstrin homology and coiled-coil domain containing D1, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 14:69484692-69531551

Links

ENSG00000175985 ∙ NCBI:400224 ∙ ∙ HGNC:20148 ∙ Uniprot:A6NEE1 ∙ 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 PLEKHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHD1 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			37	2		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					2	2
Total	0	0	37	3	2

Variants in PLEKHD1

This is a list of pathogenic ClinVar variants found in the PLEKHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-69484996-C-T		not specified	Uncertain significance (Nov 25, 2024)
14-69485089-A-G		not specified	Uncertain significance (May 28, 2024)
14-69500165-A-G		not specified	Uncertain significance (Jun 29, 2023)
14-69500199-A-G		not specified	Uncertain significance (Feb 17, 2024)
14-69500567-T-C			Benign (Jun 18, 2018)
14-69500596-G-T		not specified	Uncertain significance (Dec 10, 2024)
14-69500611-C-G		not specified	Uncertain significance (Apr 18, 2023)
14-69500654-C-G		not specified	Uncertain significance (Nov 04, 2023)
14-69500676-G-A			Benign (Jun 18, 2018)
14-69500896-C-T		not specified	Uncertain significance (Dec 09, 2023)
14-69500943-A-G		not specified	Uncertain significance (Feb 16, 2023)
14-69502838-G-A		not specified	Uncertain significance (Jan 23, 2023)
14-69502878-A-G		not specified	Uncertain significance (May 13, 2022)
14-69522293-G-A		not specified	Uncertain significance (Mar 21, 2023)
14-69522316-G-A		not specified	Uncertain significance (Jun 07, 2023)
14-69522341-T-C		not specified	Uncertain significance (Jun 02, 2023)
14-69524240-T-C		not specified	Uncertain significance (Jan 26, 2022)
14-69524303-C-T		not specified	Uncertain significance (Dec 21, 2022)
14-69524309-A-C		not specified	Uncertain significance (Apr 06, 2024)
14-69525953-A-G		not specified	Uncertain significance (Sep 25, 2024)
14-69525964-G-T		not specified	Uncertain significance (Mar 23, 2023)
14-69525986-G-A		not specified	Uncertain significance (Jun 12, 2023)
14-69526058-A-C		not specified	Uncertain significance (May 26, 2022)
14-69526113-C-T		not specified	Uncertain significance (Sep 10, 2024)
14-69526121-C-T		not specified	Uncertain significance (Jul 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHD1	protein_coding	protein_coding	ENST00000322564	13	43807

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000909	0.997	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	205	283	0.724	0.0000165	3327
Missense in Polyphen		66	85.434	0.77252		1006
Synonymous	2.39	78	110	0.710	0.00000591	921
Loss of Function	2.61	13	27.8	0.467	0.00000127	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhd1