THSD1

thrombospondin type 1 domain containing 1

Basic information

Region (hg38): 13:52377167-52416373

Links

ENSG00000136114NCBI:55901OMIM:616821HGNC:17754Uniprot:Q9NS62AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Aneurysm, intracranial berry, 12; Lymphatic malformation 13AD/ARCardiovascularIndividuals 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 managementCardiovascular26036949; 27895300; 28749478; 30055085; 33569873

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the THSD1 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
15
clinvar
4
clinvar
19
missense
1
clinvar
83
clinvar
4
clinvar
88
nonsense
3
clinvar
1
clinvar
2
clinvar
6
start loss
0
frameshift
1
clinvar
1
clinvar
1
clinvar
3
splice donor/acceptor (+/-2bp)
0
Total 4 3 86 19 4

Highest pathogenic variant AF is 0.00000991333

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
THSD1protein_codingprotein_codingENST00000258613 429325
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.55e-80.9641256770711257480.000282
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4974524830.9360.00002765572
Missense in Polyphen105122.510.857061510
Synonymous0.03472002010.9970.00001271745
Loss of Function2.041627.50.5810.00000157315

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006910.000691
Ashkenazi Jewish0.000.00
East Asian0.0002720.000272
Finnish0.0003240.000323
European (Non-Finnish)0.0002410.000193
Middle Eastern0.0002720.000272
South Asian0.0005940.000588
Other0.0006550.000489

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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