THSD1
Basic information
Region (hg38): 13:52377167-52416373
Links
Phenotypes
GenCC
Source:
- non-immune hydrops fetalis (Definitive), mode of inheritance: AR
- intracranial berry aneurysm (Supportive), mode of inheritance: AD
- aneurysm, intracranial berry, 12 (Limited), mode of inheritance: AD
- multiple congenital anomalies/dysmorphic syndrome (Limited), mode of inheritance: AR
- aneurysm, intracranial berry, 12 (Strong), mode of inheritance: AD
- lymphatic malformation 13 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Aneurysm, intracranial berry, 12; Lymphatic malformation 13 | AD/AR | Cardiovascular | Individuals with Aneurysm, intracranial berry, 12 have been described with intracranial aneurysms, some of which progressed to subarachnoid hemorrhage, and awareness may allow early diagnosis and management; Individuals with Lymphatic malformation 13 may have cardiovascular anomalies, and awareness may allow early diagnosis and management | Cardiovascular | 26036949; 27895300; 28749478; 30055085; 33569873 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (83 variants)
- THSD1-related_disorder (18 variants)
- not_provided (17 variants)
- Lymphatic_malformation_13 (6 variants)
- Non-immune_hydrops_fetalis (2 variants)
- Aneurysm,_intracranial_berry,_12 (2 variants)
- Aortic_aneurysm (1 variants)
- Vascular_dementia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the THSD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018676.4. 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 | 15 | 19 | ||||
missense | 83 | 88 | ||||
nonsense | 6 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 4 | 3 | 86 | 19 | 4 |
Highest pathogenic variant AF is 0.00000991333
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
THSD1 | protein_coding | protein_coding | ENST00000258613 | 4 | 29325 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.55e-8 | 0.964 | 125677 | 0 | 71 | 125748 | 0.000282 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.497 | 452 | 483 | 0.936 | 0.0000276 | 5572 |
Missense in Polyphen | 105 | 122.51 | 0.85706 | 1510 | ||
Synonymous | 0.0347 | 200 | 201 | 0.997 | 0.0000127 | 1745 |
Loss of Function | 2.04 | 16 | 27.5 | 0.581 | 0.00000157 | 315 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000691 | 0.000691 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000272 | 0.000272 |
Finnish | 0.000324 | 0.000323 |
European (Non-Finnish) | 0.000241 | 0.000193 |
Middle Eastern | 0.000272 | 0.000272 |
South Asian | 0.000594 | 0.000588 |
Other | 0.000655 | 0.000489 |
dbNSFP
Source:
- Pathway
- Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.878
- rvis_EVS
- 0.09
- rvis_percentile_EVS
- 60.68
Haploinsufficiency Scores
- pHI
- 0.121
- hipred
- N
- hipred_score
- 0.306
- ghis
- 0.517
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.119
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Thsd1
- Phenotype
- hematopoietic system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- thsd1
- Affected structure
- cranial vasculature
- Phenotype tag
- abnormal
- Phenotype quality
- hemorrhagic
Gene ontology
- Biological process
- Cellular component
- extracellular region;cytosol;integral component of membrane
- Molecular function