PMP2

peripheral myelin protein 2, the group of Fatty acid binding protein family

Basic information

Region (hg38): 8:81440326-81447439

Links

ENSG00000147588 ∙ NCBI:5375 ∙ OMIM:170715 ∙ HGNC:9117 ∙ Uniprot:P02689 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Charcot-Marie-Tooth disease, demyelinating, type 1G (Moderate), mode of inheritance: AD
• Charcot-Marie-Tooth disease, demyelinating, type 1G (Strong), mode of inheritance: AD
• Charcot-Marie-Tooth disease, demyelinating, type 1G (Supportive), mode of inheritance: AD
• Charcot-Marie-Tooth disease (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Charcot-Marie-Tooth disease, demyelinating, type 1G	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	26257172; 26828946; 27009151; 30249361

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PMP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PMP2 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				9	1	10
missense		3	45	7	4	59
nonsense			2			2
start loss			1			1
frameshift			1			1
inframe indel		1	2			3
splice donor/acceptor (+/-2bp)						0
splice region			4	1	1	6
non coding			1	20	4	25
Total	0	4	52	36	9

Variants in PMP2

This is a list of pathogenic ClinVar variants found in the PMP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-81443283-A-G			Benign (May 14, 2021)
8-81443386-A-G		Charcot-Marie-Tooth disease, demyelinating, type 1G	Benign (Oct 25, 2021)
8-81443401-G-A			Likely benign (Nov 12, 2024)
8-81443402-A-G		Inborn genetic diseases	Uncertain significance (Aug 07, 2023)
8-81443402-A-T			Uncertain significance (Mar 23, 2023)
8-81443403-C-T			Likely benign (Oct 07, 2024)
8-81443409-C-T		Inborn genetic diseases	Uncertain significance (May 08, 2024)
8-81443428-C-T			Uncertain significance (Mar 03, 2024)
8-81443430-C-T			Uncertain significance (Jul 01, 2024)
8-81443431-G-A			Likely benign (Sep 29, 2023)
8-81443432-C-T		PMP2-related disorder	Benign (Feb 02, 2025)
8-81443444-C-T			Uncertain significance (May 09, 2023)
8-81443446-T-C			Likely benign (Apr 09, 2024)
8-81443456-AAG-A			Likely benign (Mar 01, 2024)
8-81443456-AAGAG-A			Uncertain significance (Nov 01, 2023)
8-81443464-G-C			Likely benign (Jun 14, 2022)
8-81443478-C-G			Benign (May 15, 2021)
8-81444481-G-C			Likely benign (May 06, 2021)
8-81444482-A-C			Likely benign (May 06, 2021)
8-81444483-A-T			Likely benign (May 06, 2021)
8-81444484-G-C			Likely benign (May 06, 2021)
8-81444485-TAAAG-T			Likely benign (May 18, 2021)
8-81444488-A-G			Likely benign (Aug 23, 2022)
8-81444489-G-A			Likely benign (Oct 03, 2023)
8-81444490-A-C			Likely benign (May 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PMP2	protein_coding	protein_coding	ENST00000256103	4	7198

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00847	0.810	125722	0	8	125730	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0996	67	69.3	0.966	0.00000334	863
Missense in Polyphen		17	17.503	0.97127		247
Synonymous	0.554	22	25.6	0.861	0.00000135	241
Loss of Function	1.05	4	6.99	0.572	3.93e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000359	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in lipid transport protein in Schwann cells. May bind cholesterol. {ECO:0000269|PubMed:20421974}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway (Consensus)

Recessive Scores

• pRec: 0.364

Intolerance Scores

• loftool: 0.585
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.22

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.310
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.262

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pmp2
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: membrane organization
• Cellular component: cytoplasm;myelin sheath;extracellular exosome
• Molecular function: fatty acid binding;protein binding;cholesterol binding