HEPACAM
Basic information
Region (hg38): 11:124919205-124936412
Links
Phenotypes
GenCC
Source:
- megalencephalic leukoencephalopathy with subcortical cysts 2A (Strong), mode of inheritance: AR
- megalencephalic leukoencephalopathy with subcortical cysts (Supportive), mode of inheritance: AD
- macrocephaly-autism syndrome (Supportive), mode of inheritance: AD
- megalencephalic leukoencephalopathy with subcortical cysts 2B, remitting, with or without intellectual disability (Moderate), mode of inheritance: AD
- megalencephalic leukoencephalopathy with subcortical cysts 2B, remitting, with or without intellectual disability (Definitive), mode of inheritance: AD
- megalencephalic leukoencephalopathy with subcortical cysts 2A (Definitive), mode of inheritance: AR
- megalencephalic leukoencephalopathy with subcortical cysts 2A (Strong), mode of inheritance: AR
- megalencephalic leukoencephalopathy with subcortical cysts 2B, remitting, with or without intellectual disability (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Megalencephalic leukoencephalopathy with subcortical cysts 2B, remitting, with or without impaired intellectual development; Megalencephalic leukoencephalopathy with subcortical cysts 2A | AD/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 | Neurologic | 20517947; 21419380 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (8 variants)
- Megalencephalic leukoencephalopathy with subcortical cysts 2A (3 variants)
- Megalencephalic leukoencephalopathy with subcortical cysts 2B, remitting, with or without intellectual disability (3 variants)
- HEPACAM-related disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEPACAM 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 | 31 | 38 | ||||
missense | 91 | 103 | ||||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
inframe indel | 5 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 3 | 3 | 6 | |||
non coding | 40 | 23 | 14 | 77 | ||
Total | 8 | 8 | 138 | 56 | 22 |
Variants in HEPACAM
This is a list of pathogenic ClinVar variants found in the HEPACAM region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-124919286-G-A | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 12, 2018) | ||
11-124919286-G-C | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 12, 2018) | ||
11-124919336-A-AAAAC | Megalencephalic leukoencephalopathy with subcortical cysts | Benign (Jun 14, 2016) | ||
11-124919339-A-G | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 13, 2018) | ||
11-124919504-T-C | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 12, 2018) | ||
11-124919524-T-A | Megalencephalic leukoencephalopathy with subcortical cysts | Benign (Jan 12, 2018) | ||
11-124919659-A-G | Megalencephalic leukoencephalopathy with subcortical cysts | Likely benign (Jan 13, 2018) | ||
11-124919662-G-A | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 13, 2018) | ||
11-124919686-AG-A | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jun 14, 2016) | ||
11-124919846-AAGG-A | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jun 14, 2016) | ||
11-124919859-T-C | Megalencephalic leukoencephalopathy with subcortical cysts | Benign (Jan 13, 2018) | ||
11-124919860-G-A | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 12, 2018) | ||
11-124919903-C-T | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 12, 2018) | ||
11-124919932-A-T | Megalencephalic leukoencephalopathy with subcortical cysts | Benign (Jan 13, 2018) | ||
11-124920105-T-C | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 13, 2018) | ||
11-124920114-C-G | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 13, 2018) | ||
11-124920149-C-A | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 13, 2018) | ||
11-124920195-C-T | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Apr 27, 2017) | ||
11-124920276-G-T | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 12, 2018) | ||
11-124920307-C-A | Megalencephalic leukoencephalopathy with subcortical cysts | Likely benign (Jan 12, 2018) | ||
11-124920411-C-T | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 12, 2018) | ||
11-124920429-G-A | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 13, 2018) | ||
11-124920472-C-T | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jan 12, 2018) | ||
11-124920509-C-T | Megalencephalic leukoencephalopathy with subcortical cysts | Uncertain significance (Jun 14, 2016) | ||
11-124920666-A-C | Megalencephalic leukoencephalopathy with subcortical cysts | Likely benign (Jan 12, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
HEPACAM | protein_coding | protein_coding | ENST00000298251 | 7 | 17220 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.868 | 0.132 | 125719 | 0 | 29 | 125748 | 0.000115 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.59 | 145 | 210 | 0.691 | 0.0000126 | 2619 |
Missense in Polyphen | 55 | 84.066 | 0.65425 | 936 | ||
Synonymous | 0.189 | 89 | 91.3 | 0.975 | 0.00000560 | 899 |
Loss of Function | 3.16 | 2 | 15.4 | 0.130 | 8.99e-7 | 183 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00125 | 0.00125 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000352 | 0.0000352 |
Middle Eastern | 0.00125 | 0.00125 |
South Asian | 0.00 | 0.00 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in regulating cell motility and cell-matrix interactions. May inhibit cell growth through suppression of cell proliferation. {ECO:0000269|PubMed:15885354, ECO:0000269|PubMed:15917256}.;
- Disease
- DISEASE: Leukoencephalopathy, megalencephalic, with subcortical cysts, 2A (MLC2A) [MIM:613925]: A neurodegenerative disorder characterized by infantile-onset macrocephaly and later onset of motor deterioration, with ataxia and spasticity, seizures, and cognitive decline of variable severity. The brain appears swollen on magnetic resonance imaging with white-matter abnormalities and subcortical cysts, in all stages of the disease. {ECO:0000269|PubMed:21419380}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leukoencephalopathy, megalencephalic, with subcortical cysts, 2B (MLC2B) [MIM:613926]: A neurodegenerative disorder characterized by infantile-onset of macrocephaly and mildly delayed motor development associated with white-matter abnormalities on brain magnetic resonance imaging. The phenotype is milder that MLC2A, with better preserved cerebellar white matter and no subcortical cysts outside the temporal region. On follow-up, patients show normal or almost normal motor function. Some patients have normal intelligence, whereas others have a significant cognitive deficiency. {ECO:0000269|PubMed:21419380}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- loftool
- 0.162
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.91
Haploinsufficiency Scores
- pHI
- 0.469
- hipred
- Y
- hipred_score
- 0.630
- ghis
- 0.519
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.247
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hepacam
- 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
- cell cycle arrest;cell adhesion;cellular protein localization;regulation of growth
- Cellular component
- cytoplasm;cell-cell junction;integral component of membrane;axon
- Molecular function