SVEP1

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

Basic information

Region (hg38): 9:110365248-110579880

Previous symbols: [ "C9orf13" ]

Links

ENSG00000165124

∙ NCBI:79987 ∙ OMIM:611691 ∙ HGNC:15985 ∙ Uniprot:Q4LDE5 ∙ 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 SVEP1 gene.

not_specified (434 variants)
not_provided (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SVEP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153366.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				14 clinvar		14
missense			408 clinvar	28 clinvar		436
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	408	42	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SVEP1	protein_coding	protein_coding	ENST00000401783	48	214630

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000497	124567	0	74	124641	0.000297

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	1668	1.90e+3	0.879	0.0000984	23267
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000640	0.000382
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.00110	0.00106
Finnish	0.000190	0.000186
European (Non-Finnish)	0.000268	0.000265
Middle Eastern	0.00110	0.00106
South Asian	0.000373	0.000360
Other	0.000344	0.000330

dbNSFP

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

Haploinsufficiency Scores

pHI: 0.757
hipred: Y
hipred_score: 0.604
ghis: 0.501

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.0998

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Svep1
Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); limbs/digits/tail phenotype;

Zebrafish Information Network

Gene name: svep1
Affected structure: vascular lymphangioblast
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: cell adhesion
Cellular component: extracellular region;cytoplasm;membrane
Molecular function: chromatin binding;calcium ion binding