THSD7B

protein-coding

thrombospondin type 1 domain containing 7B

Gene summary

Predicted to be involved in actin cytoskeleton organization. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001316349.2

Inheritance

—

ClinVar variants

U:180B:6

Top phenotype

Ehlers-Danlos syndrome, classic type

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr2:136,765,545-137,677,718

External References & Databases

Ensembl (ENSG00000144229)

Transcript & Mutation Effects

hg38 • Region Span ~912.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to THSD7B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 176

not providedTotal: 1

Ehlers-Danlos syndrome, classic typeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001316349.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar		5
missense			173 clinvar	4 clinvar		177
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	180	6	0	186

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001316349.2	RefSeq	NP_001303278.1	27	MANE Select
ENST00000409968.6	Ensembl	ENSP00000387145.1	27	MANE Select
ENST00000472720.5	Ensembl	ENSP00000473349.1	2	Standard
XM_047445935.1	RefSeq	XP_047301891.1	26	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
O-glycosylation of TSR domain-containing proteins
O-linked glycosylation

Biological Process

actin cytoskeleton reorganization

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272643
Coding exons: 28
Length: 912173
Individuals with no LoFs: 124562
Homozygous LoFs: 0
Heterozygous LoFs: 95
Defined: 124657
p: 0.000381

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.737	817	879	0.930	0.0000480	10477
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00053	0.00052	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.00041	0.00040	rare
East Asian	0.00045	0.00045	rare
Finnish	0.00061	0.00060	rare
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00030	0.00029	rare
Other	0.00018	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0867

Essentials

Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0995

Gene Damage Prediction

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