SNN

stannin

Basic information

Region (hg38): 16:11668455-11679152

Links

ENSG00000184602 ∙ NCBI:8303 ∙ OMIM:603032 ∙ HGNC:11149 ∙ Uniprot:O75324 ∙ 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 SNN gene.

• not_specified (15 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003498.6. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			15			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNN	protein_coding	protein_coding	ENST00000329565	1	10746

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.144	0.643	125724	0	8	125732	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.569	49	61.6	0.796	0.00000405	561
Missense in Polyphen		30	40.26	0.74515		387
Synonymous	0.0332	29	29.2	0.992	0.00000222	190
Loss of Function	0.635	1	1.96	0.510	8.31e-8	23

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000112	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the toxic effects of organotins (PubMed:15269288). Plays a role in endosomal maturation (PubMed:27015288). {ECO:0000269|PubMed:15269288, ECO:0000269|PubMed:27015288}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.507
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.111
• hipred: Y
• hipred_score: 0.579
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0549

Mouse Genome Informatics

• Gene name: Snn

Gene ontology

• Biological process: response to toxic substance
• Cellular component: cytoplasm;mitochondrial outer membrane;integral component of membrane
• Molecular function: metal ion binding