PLEKHS1

Gene

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

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

C10orf81

MANE transcript

NM_001395068.1

Inheritance

—

ClinVar variants

U:75B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.22

Max pathogenic AF

—

Genomic locus

chr10:113,751,262-113,783,429

External References & Databases

Ensembl (ENSG00000148735)

Transcript & Mutation Effects

hg38 • Region Span ~32.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PLEKHS1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395068.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar		4
missense			71 clinvar	4 clinvar		75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	75	6	0	81

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395068.1	RefSeq	NP_001381997.1	12	MANE Select
ENST00000694986.1	Ensembl	ENSP00000511629.1	12	MANE Select
NM_001193434.2	RefSeq	NP_001180363.1	9	Standard
NM_001193435.2	RefSeq	NP_001180364.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369310
Coding exons: 12
Length: 31976
Individuals with no LoFs: 125693
Homozygous LoFs: 0
Heterozygous LoFs: 53
Defined: 125746
p: 0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.779	207	241	0.859	0.0000114	3069
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00013	rare
South Asian	0.00079	0.00078	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.33
RVIS percentile EVS: 94.17

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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