SVEP1

protein-coding

sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1, the group of Sushi domain containing

Gene summary

Enables integrin binding activity. Involved in negative regulation of vasoconstriction and positive regulation of platelet activation. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf13

MANE transcript

NM_153366.4

Inheritance

—

ClinVar variants

U:498B:44

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr9:110,365,248-110,579,880

External References & Databases

Ensembl (ENSG00000165124)

Transcript & Mutation Effects

hg38 • Region Span ~214.6 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 SVEP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 485

not providedTotal: 24

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153366.4. 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			5 clinvar	14 clinvar		19
missense			481 clinvar	30 clinvar		511
nonsense			4 clinvar			4
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	498	44	0	542

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153366.4	RefSeq	NP_699197.3	48	MANE Select
ENST00000374469.6	Ensembl	ENSP00000363593.2	48	MANE Select
ENST00000374461.1	Ensembl	ENSP00000363585.2	14	Standard
ENST00000374461.2	Ensembl	ENSP00000363585.2	14	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
svep1	Danio rerio	Structure: vascular lymphangioblast Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

svep1

Danio rerio

Structure: vascular lymphangioblast

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell adhesion

Molecular Function

chromatin binding
calcium ion binding

Cellular Component

extracellular region
cytoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000401783
Coding exons: 48
Length: 214630
Individuals with no LoFs: 124567
Homozygous LoFs: 0
Heterozygous LoFs: 74
Defined: 124641
p: 0.000297

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.88	1668	1.90e+3	0.879	0.0000984	23267
Missense (PolyPhen)		612	839.62	0.7289		10336
Synonymous	0.463	706	722	0.978	0.0000402	6792
Loss of Function	9.42	29	156	0.186	0.00000778	2068

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00032	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0011	0.0011	notable
Finnish	0.00019	0.00019	rare
European (Non-Finnish)	0.00027	0.00027	rare
South Asian	0.00037	0.00036	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in the cell attachment process. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.325
RVIS EVS: 4.59
RVIS percentile EVS: 99.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0998

Gene Damage Prediction

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