PLP2

protein-coding

proteolipid protein 2, the group of MARVEL domain containing

Gene summary

This gene encodes an integral membrane protein that localizes to the endoplasmic reticulum in colonic epithelial cells. The encoded protein can multimerize and may function as an ion channel. A polymorphism in the promoter of this gene may be linked to an increased risk of X-linked cognitive disability. A pseudogene of this gene is found on chromosome 5. [provided by RefSeq, Jan 2010]

MANE transcript

NM_002668.3

Inheritance

—

ClinVar variants

U:39B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chrX:49,171,898-49,175,235

External References & Databases

Ensembl (ENSG00000102007)

Transcript & Mutation Effects

hg38 • Region Span ~3.3 kb

Loading mutation effect viewer...

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 PLP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 18

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002668.3. 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			3 clinvar	1 clinvar		4
missense			28 clinvar	1 clinvar	1 clinvar	30
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	39	2	1	42

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002668.3	RefSeq	NP_002659.1	5	MANE Select
ENST00000376327.6	Ensembl	ENSP00000365505.5	5	MANE Select
ENST00000376322.7	Ensembl	ENSP00000365500.3	3	Standard
ENST00000376322.8	Ensembl	ENSP00000365500.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

ion transport
chemotaxis
cytokine-mediated signaling pathway
ion transmembrane transport

Molecular Function

protein binding
ion transmembrane transporter activity
chemokine binding

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
plasma membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376327
Coding exons: 5
Length: 3316
Individuals with no LoFs: 125678
Homozygous LoFs: 36
Heterozygous LoFs: 32
Defined: 125746
p: 0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.249	58	63.6	0.912	0.00000490	969
Missense (PolyPhen)		12	15.36	0.78126		279
Synonymous	0.236	27	28.6	0.944	0.00000246	326
Loss of Function	0.654	4	5.68	0.704	4.35e-7	82

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000076	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00016	rare
Finnish	0.00044	0.00032	rare
European (Non-Finnish)	0.00061	0.00044	rare
South Asian	0.00016	0.000098	rare
Other	0.00088	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in cell differentiation in the intestinal epithelium.;

Recessive Scores

pRec: 0.132

Intolerance Scores

LoFtool: 0.520
RVIS EVS: -0.01
RVIS percentile EVS: 53.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.474

Gene Damage Prediction

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