SNED1

sushi, nidogen and EGF like domains 1, the group of Sushi domain containing|Fibronectin type III domain containing

Basic information

Region (hg38): 2:240998618-241095568

Links

ENSG00000162804 ∙ NCBI:25992 ∙ OMIM:616634 ∙ HGNC:24696 ∙ Uniprot:Q8TER0 ∙ 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 SNED1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNED1 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				7	5	12
missense			74	3	2	79
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	74	10	7

Variants in SNED1

This is a list of pathogenic ClinVar variants found in the SNED1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-240998853-G-C		not specified	Uncertain significance (Oct 07, 2024)
2-240998874-G-A		not specified	Uncertain significance (May 06, 2024)
2-240998911-C-A		not specified	Uncertain significance (Mar 29, 2022)
2-240998935-C-G		not specified	Uncertain significance (Oct 08, 2024)
2-240998946-G-A		not specified	Uncertain significance (Mar 23, 2022)
2-240999001-C-T		not specified	Uncertain significance (Feb 28, 2023)
2-240999044-A-ACT			not provided (-)
2-241030315-A-G		not specified	Uncertain significance (May 08, 2023)
2-241030368-G-T		not specified	Uncertain significance (Sep 04, 2024)
2-241030402-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-241030405-G-A		not specified	Uncertain significance (Jun 16, 2024)
2-241030408-C-G		not specified	Uncertain significance (Apr 12, 2023)
2-241030413-G-A		not specified	Uncertain significance (Nov 10, 2022)
2-241030437-G-A		not specified	Uncertain significance (Aug 28, 2024)
2-241030456-G-A		not specified	Uncertain significance (Apr 08, 2024)
2-241030462-C-T		not specified	Uncertain significance (Jun 05, 2024)
2-241030464-G-A		not specified	Uncertain significance (Jun 30, 2022)
2-241030510-C-A		not specified	Uncertain significance (Oct 17, 2024)
2-241030510-C-T		not specified	Uncertain significance (Oct 25, 2024)
2-241030515-G-A		not specified	Uncertain significance (Mar 16, 2022)
2-241030525-C-G		not specified	Uncertain significance (Feb 28, 2023)
2-241030561-C-T		not specified	Uncertain significance (Jan 26, 2022)
2-241033809-G-A			Likely benign (Mar 01, 2023)
2-241033850-C-T		not specified	Uncertain significance (Dec 03, 2024)
2-241034585-C-G			Benign (Apr 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNED1	protein_coding	protein_coding	ENST00000310397	31	96729

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.662	0.338	124854	0	70	124924	0.000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.13	610	870	0.701	0.0000572	9082
Missense in Polyphen		204	361.7	0.56401		3849
Synonymous	1.37	339	373	0.910	0.0000278	2777
Loss of Function	6.06	15	69.5	0.216	0.00000355	788

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000669	0.000617
Ashkenazi Jewish	0.000101	0.0000994
East Asian	0.00157	0.00145
Finnish	0.0000496	0.0000464
European (Non-Finnish)	0.000174	0.000159
Middle Eastern	0.00157	0.00145
South Asian	0.000139	0.000131
Other	0.00117	0.00115

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.182
• rvis_EVS: -1.38
• rvis_percentile_EVS: 4.36

Haploinsufficiency Scores

• pHI: 0.224
• hipred: Y
• hipred_score: 0.623
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.212

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sned1

Gene ontology

• Biological process: cell-matrix adhesion
• Cellular component: extracellular region
• Molecular function: calcium ion binding