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.

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.

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				12		12
missense			184	16		200
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	184	28	0

Variants in SVEP1

This is a list of pathogenic ClinVar variants found in the SVEP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-110369990-C-T		not specified	Uncertain significance (Jan 04, 2024)
9-110375430-C-T		not specified	Uncertain significance (Jul 19, 2023)
9-110375437-C-T		not specified	Uncertain significance (Aug 16, 2021)
9-110375447-G-A			Likely benign (Jan 01, 2024)
9-110377324-C-T		not specified	Uncertain significance (Jan 03, 2024)
9-110377326-T-G		not specified	Uncertain significance (Jun 11, 2021)
9-110379377-C-T		not specified	Uncertain significance (Jun 18, 2021)
9-110379385-A-G		not specified	Uncertain significance (Sep 12, 2023)
9-110379479-T-C		not specified	Uncertain significance (Jun 07, 2024)
9-110385910-C-T		not specified	Uncertain significance (Nov 10, 2022)
9-110385954-C-A		not specified	Uncertain significance (Sep 16, 2021)
9-110386011-T-A		not specified	Uncertain significance (Dec 06, 2022)
9-110386043-G-A			Likely benign (Nov 01, 2022)
9-110387302-G-A		not specified	Uncertain significance (Apr 09, 2024)
9-110387306-G-C		not specified	Uncertain significance (May 24, 2023)
9-110387357-T-C		not specified	Uncertain significance (Dec 22, 2023)
9-110387368-T-A		not specified	Uncertain significance (Oct 11, 2023)
9-110387398-G-A		not specified	Uncertain significance (Sep 22, 2022)
9-110387408-C-G		not specified	Uncertain significance (Mar 19, 2024)
9-110387410-A-G		not specified	Uncertain significance (Nov 09, 2021)
9-110387425-T-C		not specified	Uncertain significance (Apr 26, 2023)
9-110389557-T-C		not specified	Likely benign (Nov 09, 2021)
9-110389574-C-T		not specified	Uncertain significance (Feb 02, 2022)
9-110389575-G-A		not specified	Uncertain significance (Jan 23, 2024)
9-110400922-C-T		not specified	Uncertain significance (May 04, 2023)

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
• 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