GPNMB
Basic information
Region (hg38): 7:23235967-23275108
Links
Phenotypes
GenCC
Source:
- amyloidosis, primary localized cutaneous, 3 (Moderate), mode of inheritance: AR
- amyloidosis, primary localized cutaneous, 3 (Strong), mode of inheritance: AR
- amyloidosis, primary localized cutaneous, 3 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Amyloidosis, primary, localized cutaneous, 3 | AR | 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 | Dermatologic | 19416385; 29336782 |
ClinVar
This is a list of variants' phenotypes submitted to
- Amyloidosis, primary localized cutaneous, 3 (4 variants)
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPNMB 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 | |||||
missense | 48 | 59 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 5 | 4 | 48 | 14 | 7 |
Highest pathogenic variant AF is 0.000164
Variants in GPNMB
This is a list of pathogenic ClinVar variants found in the GPNMB region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
7-23246865-G-T | Inborn genetic diseases | Uncertain significance (Jul 02, 2024) | ||
7-23246867-C-T | Inborn genetic diseases | Uncertain significance (Mar 01, 2024) | ||
7-23246890-G-A | GPNMB-related disorder | Benign (Dec 24, 2018) | ||
7-23246906-T-C | GPNMB-related disorder | Benign (Mar 27, 2019) | ||
7-23246910-C-T | Likely benign (Dec 31, 2019) | |||
7-23246921-G-T | Inborn genetic diseases | Uncertain significance (Oct 10, 2023) | ||
7-23246922-C-A | Inborn genetic diseases | Uncertain significance (Apr 04, 2024) | ||
7-23253412-A-C | Inborn genetic diseases | Uncertain significance (Jun 24, 2022) | ||
7-23253427-G-A | Inborn genetic diseases | Uncertain significance (Jan 31, 2022) | ||
7-23254171-G-T | Likely benign (Mar 01, 2024) | |||
7-23254202-C-T | Inborn genetic diseases | Uncertain significance (Nov 05, 2021) | ||
7-23254212-C-T | Likely benign (Dec 31, 2019) | |||
7-23254235-C-T | Benign (Sep 19, 2018) | |||
7-23254237-G-A | Inborn genetic diseases | Uncertain significance (Oct 22, 2024) | ||
7-23254239-GA-G | Amyloidosis, primary localized cutaneous, 3 | Pathogenic (Mar 27, 2018) | ||
7-23254254-TAGATGCCAAAAGGA-T | Amyloidosis, primary localized cutaneous, 3 • GPNMB-related disorder | Pathogenic/Likely pathogenic (Aug 23, 2019) | ||
7-23254279-G-A | Inborn genetic diseases | Uncertain significance (Sep 10, 2024) | ||
7-23254284-C-T | Likely benign (Feb 25, 2018) | |||
7-23256914-G-A | GPNMB-related disorder | Benign (Oct 23, 2019) | ||
7-23256917-T-G | Amyloidosis, primary localized cutaneous, 3 | Pathogenic (-) | ||
7-23256945-G-T | GPNMB-related disorder | Likely benign (Dec 31, 2019) | ||
7-23256953-C-T | GPNMB-related disorder | Benign (Feb 28, 2019) | ||
7-23256954-G-A | Inborn genetic diseases | Uncertain significance (Apr 07, 2023) | ||
7-23256993-C-T | Inborn genetic diseases | Uncertain significance (Jul 14, 2021) | ||
7-23257050-G-A | Inborn genetic diseases | Uncertain significance (Jan 25, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GPNMB | protein_coding | protein_coding | ENST00000381990 | 11 | 39142 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.88e-27 | 0.00000806 | 125403 | 1 | 344 | 125748 | 0.00137 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.124 | 318 | 324 | 0.981 | 0.0000173 | 3752 |
Missense in Polyphen | 86 | 91.99 | 0.93489 | 1142 | ||
Synonymous | 0.116 | 130 | 132 | 0.987 | 0.00000804 | 1124 |
Loss of Function | -1.35 | 36 | 28.2 | 1.27 | 0.00000161 | 302 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00230 | 0.00230 |
Ashkenazi Jewish | 0.00179 | 0.00179 |
East Asian | 0.00402 | 0.00398 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.00133 | 0.00133 |
Middle Eastern | 0.00402 | 0.00398 |
South Asian | 0.000922 | 0.000882 |
Other | 0.000816 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Could be a melanogenic enzyme. {ECO:0000250}.;
- Disease
- DISEASE: Note=Increased expression levels in glioblastoma multiforme biopsy samples correlate with poor patient survival prognosis (PubMed:16609006). Has been proposed as a potential target for antibodies coupled to cytotoxic drugs in the context of cancer immunotherapy, including that of melanoma (PubMed:16489096). {ECO:0000269|PubMed:16489096, ECO:0000269|PubMed:16609006}.; DISEASE: Amyloidosis, primary localized cutaneous, 3 (PLCA3) [MIM:617920]: A primary amyloidosis characterized by localized cutaneous amyloid deposition. This condition usually presents with itching (especially on the lower legs) and visible changes of skin hyperpigmentation and thickening that may be exacerbated by chronic scratching and rubbing. Primary localized cutaneous amyloidosis is often divided into macular and lichen subtypes although many affected individuals often show both variants coexisting. Lichen amyloidosis characteristically presents as a pruritic eruption of grouped hyperkeratotic papules with a predilection for the shins, calves, ankles and dorsa of feet and thighs. Papules may coalesce to form hyperkeratotic plaques that can resemble lichen planus, lichen simplex or nodular prurigo. Macular amyloidosis is characterized by small pigmented macules that may merge to produce macular hyperpigmentation, sometimes with a reticulate or rippled pattern. In macular and lichen amyloidosis, amyloid is deposited in the papillary dermis in association with grouped colloid bodies, thought to represent degenerate basal keratinocytes. The amyloid deposits probably reflect a combination of degenerate keratin filaments, serum amyloid P component, and deposition of immunoglobulins. PLCA3 inheritance is autosomal recessive. {ECO:0000269|PubMed:29336782}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Signaling by PTK6;Signal Transduction;PTK6 promotes HIF1A stabilization;Signaling by Non-Receptor Tyrosine Kinases
(Consensus)
Recessive Scores
- pRec
- 0.135
Intolerance Scores
- loftool
- 0.984
- rvis_EVS
- 0.89
- rvis_percentile_EVS
- 89.29
Haploinsufficiency Scores
- pHI
- 0.702
- hipred
- N
- hipred_score
- 0.180
- ghis
- 0.445
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.186
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gpnmb
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; neoplasm; pigmentation 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); vision/eye phenotype; homeostasis/metabolism phenotype; immune system phenotype;
Gene ontology
- Biological process
- osteoblast differentiation;negative regulation of cytokine production;positive regulation of protein phosphorylation;cell adhesion;signal transduction;cell-cell signaling;negative regulation of cell population proliferation;regulation of signaling receptor activity;bone mineralization;positive regulation of cell migration;positive regulation of protein autophosphorylation;negative regulation of tumor necrosis factor production;regulation of tissue remodeling;negative regulation of T cell proliferation;regulation of angiogenesis;negative regulation of T cell activation;positive chemotaxis;positive regulation of ERK1 and ERK2 cascade;negative regulation of neuron death;negative regulation of G1/S transition of mitotic cell cycle
- Cellular component
- plasma membrane;integral component of plasma membrane;integral component of membrane;early endosome membrane;melanosome membrane
- Molecular function
- integrin binding;protein binding;heparin binding;chemoattractant activity;syndecan binding;receptor ligand activity