PMEL

premelanosome protein

Basic information

Region (hg38): 12:55954105-55973317

Previous symbols: [ "SIL", "SILV" ]

Links

ENSG00000185664

∙ NCBI:6490 ∙ OMIM:155550 ∙ HGNC:10880 ∙ Uniprot:P40967 ∙ 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 PMEL gene.

not_specified (59 variants)
not_provided (12 variants)
PMEL-related_disorder (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PMEL gene is commonly pathogenic or not. These statistics are base on transcript: NM_001384361.1. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	1 clinvar	5
missense			53 clinvar	6 clinvar	7 clinvar	66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	10	8

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PMEL	protein_coding	protein_coding	ENST00000449260	11	19213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.06e-18	0.00883	125594	0	154	125748	0.000613

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.894	322	370	0.869	0.0000186	4260
Missense in Polyphen		123	140.9	0.87297		1724
Synonymous	-0.132	148	146	1.01	0.00000747	1473
Loss of Function	0.310	28	29.8	0.939	0.00000153	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00110
Ashkenazi Jewish	0.000894	0.000893
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000916	0.000915
Middle Eastern	0.000109	0.000109
South Asian	0.000392	0.000392
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a central role in the biogenesis of melanosomes. Involved in the maturation of melanosomes from stage I to II. The transition from stage I melanosomes to stage II melanosomes involves an elongation of the vesicle, and the appearance within of distinct fibrillar structures. Release of the soluble form, ME20-S, could protect tumor cells from antibody mediated immunity. {ECO:0000269|PubMed:11694580, ECO:0000269|PubMed:21962903}.;

Recessive Scores

pRec: 0.319

Intolerance Scores

loftool
rvis_EVS: -0.04
rvis_percentile_EVS: 50.51

Haploinsufficiency Scores

pHI: 0.530
hipred: N
hipred_score: 0.123
ghis: 0.395

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pmel
Phenotype: pigmentation phenotype; vision/eye phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Zebrafish Information Network

Gene name: pmelb
Affected structure: retinal pigmented epithelium
Phenotype tag: abnormal
Phenotype quality: morphology

Gene ontology

Biological process: melanosome organization;melanin biosynthetic process
Cellular component: extracellular region;endoplasmic reticulum membrane;Golgi apparatus;plasma membrane;integral component of plasma membrane;multivesicular body membrane;melanosome
Molecular function: protein binding;identical protein binding