PLP2

proteolipid protein 2, the group of MARVEL domain containing

Basic information

Region (hg38): X:49171898-49175235

Links

ENSG00000102007 ∙ NCBI:5355 ∙ OMIM:300112 ∙ HGNC:9087 ∙ Uniprot:Q04941 ∙ 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 PLP2 gene.

• not_specified (17 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002668.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			16	1	1	18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	2	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLP2	protein_coding	protein_coding	ENST00000376327	5	3316

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00439	0.686	125678	36	32	125746	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.249	58	63.6	0.912	0.00000490	969
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000760	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000216	0.000163
Finnish	0.000439	0.000323
European (Non-Finnish)	0.000610	0.000440
Middle Eastern	0.000216	0.000163
South Asian	0.000157	0.0000980
Other	0.000882	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.344
• hipred: N
• hipred_score: 0.343
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.474

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plp2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: ion transport;chemotaxis;cytokine-mediated signaling pathway;ion transmembrane transport
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane
• Molecular function: protein binding;ion transmembrane transporter activity;chemokine binding