GeneBe

THSD7A

thrombospondin type 1 domain containing 7A

Basic information

Region (hg38): 7:11370365-11832198

Links

ENSG00000005108 ∙ NCBI:221981 ∙ OMIM:612249 ∙ HGNC:22207 ∙ Uniprot:Q9UPZ6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the THSD7A gene.

  • not_specified (248 variants)
  • not_provided (23 variants)
  • THSD7A-related_disorder (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THSD7A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015204.3. 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
7
clinvar
6
clinvar
 13
missense
243
clinvar
10
clinvar
1
clinvar
 254
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total 0 0 244 17 7
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
THSD7Aprotein_codingprotein_codingENST00000423059 28461841
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.005.65e-71246190271246460.000108
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5989478971.060.000048610780
Missense in Polyphen239289.080.826753239
Synonymous-3.114053331.220.00001893058
Loss of Function8.06141020.1380.000005531115

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001880.000187
Ashkenazi Jewish0.000.00
East Asian0.00005580.0000556
Finnish0.000.00
European (Non-Finnish)0.0001610.000159
Middle Eastern0.00005580.0000556
South Asian0.0001640.000163
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Thrombospondin type-1 domain-containing protein 7A: Plays a role in actin cytoskeleton rearrangement. {ECO:0000269|PubMed:27214550}.;
Disease
DISEASE: Note=Autoantibodies against THSD7A have been detected in serum and glomeruli from patients with idiopathic membranous nephropathy (PubMed:25394321). The majority of the autoantibodies react with the two most N-terminal TSP type-1 domains (PubMed:29555830). {ECO:0000269|PubMed:25394321, ECO:0000269|PubMed:29555830}.;
Pathway
Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

pRec
0.0894

Intolerance Scores

loftool
rvis_EVS
-1.31
rvis_percentile_EVS
4.87

Haploinsufficiency Scores

pHI
0.274
hipred
Y
hipred_score
0.600
ghis
0.524

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.237

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Thsd7a
Phenotype

Zebrafish Information Network

Gene name
thsd7aa
Affected structure
endothelial tip cell
Phenotype tag
abnormal
Phenotype quality
morphology

Gene ontology

Biological process
angiogenesis;cell differentiation;actin cytoskeleton reorganization
Cellular component
extracellular region;plasma membrane;integral component of membrane;cell projection
Molecular function