PLEKHS1

pleckstrin homology domain containing S1, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 10:113751261-113783429

Previous symbols: [ "C10orf81" ]

Links

ENSG00000148735 ∙ NCBI:79949 ∙ ∙ HGNC:26285 ∙ Uniprot:Q5SXH7 ∙ 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 PLEKHS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHS1 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			34	3		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	4	0

Variants in PLEKHS1

This is a list of pathogenic ClinVar variants found in the PLEKHS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-113766442-A-C		not specified	Uncertain significance (Jun 11, 2021)
10-113766463-T-A		not specified	Uncertain significance (Dec 01, 2022)
10-113766621-A-G		not specified	Uncertain significance (Aug 30, 2022)
10-113766652-G-A		not specified	Uncertain significance (Oct 17, 2023)
10-113766687-C-T		not specified	Uncertain significance (Jan 22, 2024)
10-113767352-A-G		not specified	Uncertain significance (Dec 21, 2022)
10-113767356-T-C		not specified	Uncertain significance (Jul 06, 2021)
10-113767436-A-C		not specified	Uncertain significance (Jul 13, 2021)
10-113767436-A-G		not specified	Uncertain significance (Nov 22, 2022)
10-113767458-A-G		not specified	Uncertain significance (Jun 19, 2024)
10-113767463-C-T		not specified	Uncertain significance (Dec 06, 2022)
10-113768855-C-T		not specified	Likely benign (Jan 24, 2023)
10-113768856-G-T		not specified	Likely benign (Jul 15, 2021)
10-113768871-C-G		not specified	Uncertain significance (Mar 19, 2024)
10-113769821-A-G		not specified	Uncertain significance (May 07, 2024)
10-113769849-C-A		not specified	Uncertain significance (Dec 20, 2021)
10-113771972-T-A		not specified	Uncertain significance (Aug 31, 2022)
10-113771995-G-A		not specified	Uncertain significance (Dec 01, 2022)
10-113772013-T-C		not specified	Uncertain significance (May 03, 2023)
10-113772076-G-A		not specified	Uncertain significance (Jun 29, 2023)
10-113774304-T-G		not specified	Uncertain significance (Apr 08, 2024)
10-113774836-G-C		not specified	Uncertain significance (Dec 07, 2021)
10-113774892-G-C		not specified	Uncertain significance (Jan 03, 2024)
10-113774900-A-G		not specified	Uncertain significance (Mar 02, 2023)
10-113774913-C-T			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHS1	protein_coding	protein_coding	ENST00000369310	12	31976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.14e-22	0.000117	125693	0	53	125746	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.779	207	241	0.859	0.0000114	3069
Missense in Polyphen		59	67.026	0.88026		904
Synonymous	-0.154	86	84.2	1.02	0.00000409	843
Loss of Function	-1.00	30	24.6	1.22	0.00000120	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000396	0.000395
Ashkenazi Jewish	0.00	0.00
East Asian	0.000166	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000135	0.000132
Middle Eastern	0.000166	0.000163
South Asian	0.000789	0.000784
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.17

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhs1

Gene ontology

• Molecular function: protein binding