THSD7B

thrombospondin type 1 domain containing 7B

Basic information

Region (hg38): 2:136765544-137677718

Links

ENSG00000144229 ∙ NCBI:80731 ∙ ∙ HGNC:29348 ∙ Uniprot:Q9C0I4 ∙ 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 THSD7B gene.

• Inborn genetic diseases (51 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THSD7B 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						0
missense			49	1		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	49	2	0

Variants in THSD7B

This is a list of pathogenic ClinVar variants found in the THSD7B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-136990929-A-G		not specified	Likely benign (Nov 03, 2022)
2-137056455-G-A		not specified	Uncertain significance (Mar 07, 2024)
2-137056491-G-T		not specified	Uncertain significance (Dec 18, 2023)
2-137056602-G-A		not specified	Uncertain significance (Aug 15, 2023)
2-137056644-G-A		not specified	Uncertain significance (Oct 02, 2023)
2-137056656-C-G		not specified	Uncertain significance (Nov 09, 2021)
2-137056669-A-G		not specified	Uncertain significance (Feb 16, 2023)
2-137056818-T-A		not specified	Uncertain significance (Oct 03, 2022)
2-137057140-A-G		not specified	Uncertain significance (Oct 06, 2021)
2-137057149-C-T		not specified	Uncertain significance (Mar 25, 2022)
2-137094970-A-G		not specified	Uncertain significance (Jan 02, 2024)
2-137095018-C-T		not specified	Uncertain significance (Oct 05, 2023)
2-137095043-G-C		not specified	Uncertain significance (Feb 28, 2024)
2-137095054-G-A		not specified	Uncertain significance (Apr 25, 2022)
2-137095082-C-A		not specified	Uncertain significance (Oct 18, 2021)
2-137095097-G-A		not specified	Uncertain significance (Oct 17, 2023)
2-137115204-C-T		not specified	Uncertain significance (Feb 17, 2024)
2-137160251-G-A		not specified	Uncertain significance (Feb 06, 2024)
2-137160276-A-T		not specified	Uncertain significance (Jul 14, 2021)
2-137160291-C-T		not specified	Uncertain significance (May 02, 2023)
2-137170758-C-T		not specified	Uncertain significance (Apr 12, 2023)
2-137170809-G-A		not specified	Uncertain significance (Sep 15, 2021)
2-137170920-G-A		not specified	Uncertain significance (Oct 12, 2021)
2-137170930-A-G		not specified	Uncertain significance (Jan 05, 2022)
2-137231118-A-T		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THSD7B	protein_coding	protein_coding	ENST00000272643	28	912173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.65e-19	1.00	124562	0	95	124657	0.000381

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.737	817	879	0.930	0.0000480	10477
Missense in Polyphen		114	128.17	0.88945		1349
Synonymous	-1.50	344	310	1.11	0.0000173	3009
Loss of Function	4.52	47	94.4	0.498	0.00000510	1059

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000914	0.000900
Ashkenazi Jewish	0.000414	0.000398
East Asian	0.000446	0.000445
Finnish	0.000607	0.000603
European (Non-Finnish)	0.000364	0.000345
Middle Eastern	0.000446	0.000445
South Asian	0.000296	0.000294
Other	0.000178	0.000165

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: 0.0867

Haploinsufficiency Scores

• pHI: 0.335
• hipred: N
• hipred_score: 0.487

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thsd7b

Gene ontology

• Biological process: actin cytoskeleton reorganization
• Cellular component: plasma membrane;integral component of membrane