eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| gm2 gangliosidosis, ab variant | ||||
| Disease ID | 1349 |
|---|---|
| Disease | gm2 gangliosidosis, ab variant |
| Definition | A progressive neurodegenerative disorder that begins with muscle weakness, then progresses to startle reaction, retardation and seizures. It is characterized by the accumulation of G(M2) GANGLIOSIDE in neurons that is caused by a lack of G(M2) ACTIVATOR PROTEIN function. The AB variant designation refers to the increase of both HEXOSAMINIDASE A and HEXOSAMINIDASE B in tissues that lack of G(M2) activator protein. |
| Synonym | ab variant ab variant gangliosidosis gm2 ab variant gm2 gangliosidosis ab variant gm2-gangliosidoses ab variant gm2-gangliosidosis activator deficiencies, gm2 activator deficiencies, hexosaminidase activator deficiency gm2 gangliosidosis activator deficiency, gm2 activator deficiency, hexosaminidase activator deficient tay sachs disease activator-deficient tay-sachs disease activator-deficient tay-sachs diseases defic dis gm2 protein activator deficiencies, gm2 activator deficiencies, hexosaminidase activator deficiency disease, gm2 protein activator deficiency, gm2 activator deficiency, hexosaminidase activator disease, activator-deficient tay-sachs diseases, activator-deficient tay-sachs gangliosidosis gm 02 ab variant gangliosidosis gm 02 type ab gangliosidosis gm2, ab variant gangliosidosis gm2, type ab gm protein activator deficiencey disease 02 gm2 activator defic dis gm2 activator deficiencies gm2 activator deficiency gm2 activator deficiency disease gm2 gangliosidosis, type ab gm2 protein activator defic dis gm2 protein activator deficiency disease gm2-gangliosidoses, ab variant gm2-gangliosidosis, ab variant gm2 gangliosidosis, type ab gm>2< gangliosidosis, type ab hexosaminidase activator deficiencies hexosaminidase activator deficiency hexosaminidase activator protein defic dis hexosaminidase activator protein deficiency disease tay sachs disease, ab variant tay-sachs disease, ab variant tay-sachs disease, ab variant [disease/finding] tay-sachs disease, activator-deficient tay-sachs disease, variant ab tay-sachs disease, variant ab (disorder) tay-sachs diseases, activator-deficient variant gm2-gangliosidoses, ab variant gm2-gangliosidosis, ab |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C0268275 |
| MeSH | |
| SNOMED-CT | |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:1) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | (Waiting for update.) |
| Locus | Symbol | Locus(Total Locus:1) GM2A | 5q33.1 |
| Disease ID | 1349 |
|---|---|
| Disease | gm2 gangliosidosis, ab variant |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:35) HP:0002421 | Poor head control HP:0002835 | Aspiration HP:0100543 | Cognitive impairment HP:0004322 | Short stature HP:0007256 | Abnormal pyramidal signs HP:0030904 | Glabellar reflex HP:0002267 | Exaggerated startle response HP:0002376 | Developmental regression HP:0002072 | Chorea HP:0000719 | Inappropriate behavior HP:0008897 | Postnatal growth retardation HP:0003470 | Inability to move HP:0000618 | Blindness HP:0001332 | Dystonia HP:0010729 | Cherry red spot of the macula HP:0000739 | Anxiety HP:0001276 | Hypertonia HP:0002371 | Loss of speech HP:0001252 | Hypotonia HP:0001250 | Seizures HP:0002059 | Cerebral atrophy HP:0001263 | Developmental retardation HP:0000741 | Apathy HP:0002478 | Progressive spastic quadriplegia HP:0000726 | Dementia HP:0002180 | Neurodegeneration HP:0010780 | Hyperacusis HP:0100852 | Abnormal fear/anxiety-related behavior HP:0030081 | Punctate periventricular T2 hyperintense foci HP:0001347 | Hyperreflexia HP:0003495 | GM2-ganglioside accumulation HP:0009062 | Infantile axial hypotonia HP:0002200 | Pseudobulbar signs HP:0012547 | Abnormal involuntary eye movements HP:0002476 | Primitive reflex |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:1) |
| Disease ID | 1349 |
|---|---|
| Disease | gm2 gangliosidosis, ab variant |
| Manually Symptom | (Waiting for update.) |
| Text Mined Symptom | (Waiting for update.) |
Manually Genotype(Total Text Mining Genotypes:0) |
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| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:3) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs104893892 | NA | 2760 | GM2A | umls:C0268275 | CLINVAR | NA | 0.560271442 | NA | GM2A | 5 | 151267375 | G | A,C |
| rs104893897 | NA | 2760 | GM2A | umls:C0268275 | CLINVAR | NA | 0.560271442 | NA | GM2A | 5 | 151259833 | G | T |
| rs137852797 | NA | 2760 | GM2A | umls:C0268275 | CLINVAR | NA | 0.560271442 | NA | GM2A | 5 | 151266899 | T | C |
GWASdb Annotation(Total Genotypes:5) | |||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | Pos | SNP_Id | RefGene | EnsemblGene | ENCODE_Factor | ENCODE_TFBS | Chromosome_interaction | GTEx_eQTL | SNP_TFBS_affinity_GWAS3D | SNP_miRNA_target_affinity_PolymiRTS | SNP_splicing_effect_Skippy | SNP_splicing_effect_MutPred_Splice | SNP_ns_protein_effect_dbNSFP | SNP_syn_effect_Silva | SNP_phosphorylation_effect_PhosSNP | PhastCons_score | PhyloP_score | GERP++_RS | Segway_state | Ancestral_allele | ESP_AF | ESP_AFR | ESP_AFR | ESP_EUR | TG_ASN | TG_AMR | TG_AFR | TG_EUR | Type | Consequence | bStatistic | EncH3K27Ac | EncH3K4Me1 | EncH3K4Me3 | EncNucleo | OMIM | Clinvar |
| 5 | 150635429 | rs152266 | NM_000405,GM2A | NM_001167607,GM2A | ENST00000523466,ENSG00000196743 | ENST00000357164,ENSG00000196743 | TFP.SPI1 | MCV-2 | TFP.TBP | TFP.IRF4 | TFP.GATA2 | NA | chr5,150630001,150640000,chr16,2720001,2730000,41,Hi-C | NA | Aft1-primary,1.8544 | Irx5_2385,1.4873 | Mig2-primary,1.3017 | Mig3-primary,1.3747 | Tec1-primary,1.8387 | NA | NA | NA | NA | NA | NA | 0.000 | -0.395 | -1.87 | GM1 | A | NA | NA | NA | NA | NA | NA | NA |
| 5 | 150639162 | rs16838 | NM_000405,GM2A | NM_001167607,GM2A | ENST00000523466,ENSG00000196743 | ENST00000357164,ENSG00000196743 | ENST00000523004,ENSG00000196743 | MCV-1 | NA | chr5,150630001,150640000,chr16,2720001,2730000,41,Hi-C | NA | LM153,1.6203 | LM193,1.4015 | LM214,1.2862 | NR1H2-RXRA,8.0897 | NA | NA | NA | NA | NA | NA | 0.000 | 0.070 | 0.237 | R2 | G | NA | NA | NA | NA | NA | NA | NA | NA | Transcript | INTRONIC | 850 |
| 5 | 150639778 | rs153479 | NM_000405,GM2A | NM_001167607,GM2A | ENST00000523466,ENSG00000196743 | ENST00000357164,ENSG00000196743 | ENST00000523004,ENSG00000196743 | NA | NA | chr5,150630001,150640000,chr16,2720001,2730000,41,Hi-C | NA | Barx1_2877,1.9203 | Cutl1_3494,3.9217 | Emx2_3420,4.231 | Evx1_3952,1.3291 | Evx1_3952,3.1557 | NA | NA | NA | NA | NA | NA | 0.000 | 0.472 | 1.28 | TF1 | G | NA | NA | NA | 0.580 | 0.660 | 0.640 | 0.470 | 0.550 | Transcript | INTRONIC |
| 5 | 150642265 | rs6579845 | NM_000405,GM2A | NM_001167607,GM2A | ENST00000523466,ENSG00000196743 | ENST00000357164,ENSG00000196743 | ENST00000523004,ENSG00000196743 | MCV-1 | NA | chr5,150640001,150650000,chr5,150620001,150630000,27,Hi-C | chr5,150640001,150650000,chr9,140460001,140470000,11,Hi-C | NA | Sip4-primary,1.4093 | LM9,1.8562 | LM124,1.8955 | LM135,39.168 | LM216,1.2854 | NA | NA | NA | NA | NA | NA | 0.000 | -1.317 | -3.82 | R5 | A | NA | NA | NA | NA | NA | NA | NA | NA | Transcript |
| 5 | 150646780 | rs2075783 | NM_000405,GM2A | NM_001167607,GM2A | ENST00000523466,ENSG00000196743 | ENST00000357164,ENSG00000196743 | ENST00000523004,ENSG00000196743 | NA | NA | chr5,150640001,150650000,chr5,150620001,150630000,27,Hi-C | chr5,150640001,150650000,chr9,140460001,140470000,11,Hi-C | NA | LM20,2.4872 | LM57,56.61 | LM59,4.4478 | LM90,15.696 | LM90,8.1245 | NA | NA | NA | NA | NA | NA | 0.000 | -0.915 | -5.6 | TF2 | A | NA | NA | NA | 0.240 | 0.260 | 0.380 | 0.030 | 0.300 | Transcript |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:9) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0008897 | Postnatal growth retardation | MP:0011109 | lethality throughout fetal growth and development, incomplete penetrance | the appearance of lower than Mendelian ratios of organisms of a given genotype due to death of some, but not all of the organisms between the completion of organogenesis and birth (Mus: E14 to approximately E18.5) |
| HP:0007256 | Abnormal pyramidal signs | MP:0009940 | abnormal hippocampus pyramidal cell morphology | any structural anomaly of a multipolar projection neuron in the hippocampus pyramidal cell layer; pyramidal cells have a pyramid-shaped soma with the apex and an apical dendrite pointed toward the pial surface and other dendrites and an axon emerging from |
| HP:0002421 | Poor head control | MP:0011495 | abnormal head shape | any anomaly in the characteristic surface outline or contour of a head of an organism |
| HP:0002059 | Cerebral atrophy | MP:0012506 | brain atrophy | acquired diminution of the size of the brain associated with wasting as from death and reabsorbtion of cells, diminished cellular proliferation, decreased cellular volume, pressure, ischemia, malnutrition, reduced function or malfunction, or hormonal chan |
| HP:0002267 | Exaggerated startle response | MP:0002862 | altered righting response | altered ability or changed amount of time needed to recover from an unnatural position to a normal position and/or to resist any force acting to place an organism into a false position |
| HP:0001263 | Global developmental delay | MP:0002084 | abnormal developmental patterning | abnormal systematic arrangement of the developing body along an axis |
| HP:0001252 | Muscular hypotonia | MP:0004144 | hypotonia | decreased muscle tension resulting in limpness of the muscles in the resting state, not to be confused with weakness |
| HP:0010729 | Cherry red spot of the macula | MP:0005060 | accumulation of giant lysosomes in kidney/renal tubule cells | buildup of contents in lysosomes in cells of the kidney tubules |
| HP:0002371 | Loss of speech | MP:0009403 | increased variability of skeletal muscle fiber size | greater range or dispersion within a distribution of skeletal muscle fiber size within a muscle compared to controls |
Mapped by homologous gene(Total Items:31) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0001252 | Muscular hypotonia | MP:3000003 | abnormal Ebner's gland morphology | any structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l |
| HP:0002421 | Poor head control | MP:0013504 | increased embryonic tissue cell apoptosis | increase in the timing or the number of cells in embryonic tissue undergoing programmed cell death |
| HP:0000739 | Anxiety | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0003495 | GM2-ganglioside accumulation | MP:0009969 | abnormal cerebral cortex pyramidal cell morphology | any structural anomaly of the projection neurons in the pyramidal cell layer of the cerebral cortex |
| HP:0008897 | Postnatal growth retardation | MP:3000003 | abnormal Ebner's gland morphology | any structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l |
| HP:0002476 | Primitive reflexes (palmomental, snout, glabellar) | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0001250 | Seizures | MP:3000003 | abnormal Ebner's gland morphology | any structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l |
| HP:0002267 | Exaggerated startle response | MP:0012146 | increased b wave amplitude | increase in the size (height or maximum displacement) of the b wave as measured in the electroretinogram |
| HP:0000741 | Apathy | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0001347 | Hyperreflexia | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0004322 | Short stature | MP:3000003 | abnormal Ebner's gland morphology | any structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l |
| HP:0002835 | Aspiration | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0100543 | Cognitive impairment | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0000618 | Blindness | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002478 | Progressive spastic quadriplegia | MP:0013438 | dysmyelination | reduced amount of myelin present in the form of a myelin sheath surrounding an axon due to defects in the synthesis and formation of myelin |
| HP:0002200 | Pseudobulbar signs | MP:0020157 | abnormal behavioral response to alcohol | any anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior |
| HP:0003470 | Paralysis | MP:0013659 | abnormal erythroid lineage cell morphology | any structural anomaly of an immature or mature cell in the lineage leading to and including erythrocytes |
| HP:0000719 | Inappropriate behavior | MP:0011100 | preweaning lethality, complete penetrance | death of all organisms of a given genotype in a population between fertilization and weaning age (Mus: approximately 3-4 weeks of age) |
| HP:0010729 | Cherry red spot of the macula | MP:0014185 | cerebellum atrophy | acquired diminution of the size of the cerebellum associated with wasting as from death and reabsorption of cells, diminished cellular proliferation, decreased cellular volume, pressure, ischemia, malnutrition, reduced function or malfunction, or hormonal |
| HP:0007256 | Abnormal pyramidal signs | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001263 | Global developmental delay | MP:3000003 | abnormal Ebner's gland morphology | any structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l |
| HP:0010780 | Hyperacusis | MP:0014124 | increased amylin secretion | greater than normal production or release of the polypeptide hormone that is normally co-secreted with insulin by the beta cells of the pancreatic islets of Langerhans and is known to inhibit glucagon secretion, delay gastric emptying, and act as a satiet |
| HP:0001276 | Hypertonia | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0002376 | Developmental regression | MP:0020214 | susceptible to malignant hyperthermia | increased susceptibility to hyperthermia triggered by exposure to certain drugs used for general anesthesia, specifically the volatile anesthetic agents and the neuromuscular blocking agent, succinylcholine |
| HP:0001332 | Dystonia | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0100852 | Abnormal fear/anxiety-related behavior | MP:0011109 | lethality throughout fetal growth and development, incomplete penetrance | the appearance of lower than Mendelian ratios of organisms of a given genotype due to death of some, but not all of the organisms between the completion of organogenesis and birth (Mus: E14 to approximately E18.5) |
| HP:0000726 | Dementia | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0002072 | Chorea | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0002059 | Cerebral atrophy | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002371 | Loss of speech | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0002180 | Neurodegeneration | MP:0013405 | increased circulating lactate level | greater amount of lactate in the blood which is produced from pyruvate by lactate dehydrogenase |
| Disease ID | 1349 |
|---|---|
| Disease | gm2 gangliosidosis, ab variant |
| Case | (Waiting for update.) |