SNED1

protein-coding

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

Gene summary

Predicted to enable Notch binding activity. Predicted to be involved in cell-matrix adhesion. Located in extracellular matrix. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001080437.3

Inheritance

—

ClinVar variants

U:235B:23

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr2:240,998,618-241,095,568

External References & Databases

Ensembl (ENSG00000162804)

Transcript & Mutation Effects

hg38 • Region Span ~97.0 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 SNED1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 221

not providedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080437.3. 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			4 clinvar	8 clinvar	5 clinvar	17
missense			228 clinvar	9 clinvar	1 clinvar	238
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	235	17	6	258

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080437.3	RefSeq	NP_001073906.1	31	MANE Select
ENST00000310397.13	Ensembl	ENSP00000308893.8	31	MANE Select
ENST00000401644.6	Ensembl	ENSP00000384789.2	8	Standard
ENST00000401884.5	Ensembl	ENSP00000384871.1	27	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell-matrix adhesion

Molecular Function

calcium ion binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310397
Coding exons: 31
Length: 96729
Individuals with no LoFs: 124854
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 124924
p: 0.000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.13	610	870	0.701	0.0000572	9082
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00044	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0016	0.0014	notable
Finnish	0.000050	0.000046	rare
European (Non-Finnish)	0.00017	0.00016	rare
South Asian	0.00014	0.00013	rare
Other	0.0012	0.0012	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.133

Intolerance Scores

LoFtool: 0.182
RVIS EVS: -1.38
RVIS percentile EVS: 4.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.212

Gene Damage Prediction

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