PLEKHB1

protein-coding

pleckstrin homology domain containing B1, the group of Pleckstrin homology domain containing

Gene summary

Predicted to enable protein homodimerization activity. Predicted to be involved in regulation of cell differentiation. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PHRET1

MANE transcript

NM_021200.3

Inheritance

—

ClinVar variants

U:57B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr11:73,646,178-73,662,819

External References & Databases

Ensembl (ENSG00000021300)

Transcript & Mutation Effects

hg38 • Region Span ~16.6 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 PLEKHB1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 53

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021200.3. 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			1 clinvar			1
missense			52 clinvar	1 clinvar		53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	57	1	0	58

Loading ClinVar variants...

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_021200.3	RefSeq	NP_067023.1	8	MANE Select
ENST00000354190.10	Ensembl	ENSP00000346127.5	8	MANE Select
NM_001130033.2	RefSeq	NP_001123505.1	7	Standard
NM_001130034.2	RefSeq	NP_001123506.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

multicellular organism development
phototransduction
regulation of cell differentiation

Molecular Function

protein binding

Cellular Component

cytoplasm
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000354190
Coding exons: 8
Length: 16642
Individuals with no LoFs: 124608
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 124646
p: 0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.412	148	163	0.909	0.0000108	1536
Missense (PolyPhen)		78	81.38	0.95847		759
Synonymous	0.232	69	71.5	0.965	0.00000512	497
Loss of Function	1.59	8	14.5	0.550	7.06e-7	156

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000079	0.000065	rare
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000097	0.000088	rare
South Asian	0.00013	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.132

Intolerance Scores

LoFtool: 0.553
RVIS EVS: -0.54
RVIS percentile EVS: 20.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.158

Gene Damage Prediction

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