THSD7A

thrombospondin type 1 domain containing 7A

Basic information

Region (hg38): 7:11370364-11832198

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.

• Inborn genetic diseases (80 variants)
• not provided (23 variants)
• THSD7A-related condition (2 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.

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				5	6	11
missense			80	5	1	86
nonsense						0
start loss						0
frameshift			1			1
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				3		3
Total	0	0	81	14	8

Variants in THSD7A

This is a list of pathogenic ClinVar variants found in the THSD7A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-11375804-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-11375812-A-G			Benign (Jun 27, 2018)
7-11375823-A-C		not specified	Uncertain significance (Jan 03, 2024)
7-11375852-C-T		not specified	Uncertain significance (Feb 27, 2024)
7-11375882-TA-T			Benign (Dec 31, 2019)
7-11376588-G-C		not specified	Uncertain significance (Mar 16, 2022)
7-11376610-C-A		not specified	Uncertain significance (Jan 03, 2024)
7-11376653-C-T			Likely benign (Jun 01, 2022)
7-11379084-T-C		not specified	Uncertain significance (Aug 10, 2021)
7-11379091-A-ACCAGG		THSD7A-related disorder	Uncertain significance (Apr 13, 2023)
7-11379138-T-G		not specified	Uncertain significance (Aug 08, 2022)
7-11379180-A-G		not specified	Uncertain significance (Mar 16, 2022)
7-11379199-C-T		not specified	Uncertain significance (Aug 02, 2021)
7-11379273-G-T			Likely benign (Dec 13, 2018)
7-11379632-C-T		not specified	Uncertain significance (Feb 16, 2023)
7-11379650-G-A		not specified	Uncertain significance (Jun 27, 2022)
7-11379660-C-T			Benign (Feb 20, 2018)
7-11382583-C-G		not specified	Uncertain significance (Sep 12, 2023)
7-11401844-C-G		not specified	Uncertain significance (Jul 26, 2021)
7-11406341-T-A		not specified	Uncertain significance (Jul 12, 2023)
7-11406403-A-T			Likely benign (Jun 19, 2018)
7-11406470-G-A		not specified	Uncertain significance (Mar 11, 2022)
7-11406947-C-T			Benign (Apr 04, 2018)
7-11407029-T-C		not specified	Uncertain significance (Sep 22, 2023)
7-11407031-A-G		THSD7A-related disorder	Likely benign (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THSD7A	protein_coding	protein_coding	ENST00000423059	28	461841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.65e-7	124619	0	27	124646	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.598	947	897	1.06	0.0000486	10780
Missense in Polyphen		239	289.08	0.82675		3239
Synonymous	-3.11	405	333	1.22	0.0000189	3058
Loss of Function	8.06	14	102	0.138	0.00000553	1115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000188	0.000187
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000161	0.000159
Middle Eastern	0.0000558	0.0000556
South Asian	0.000164	0.000163
Other	0.00	0.00

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

• 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Thsd7a

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