SNN

protein-coding

stannin

Gene summary

Enables metal ion binding activity. Predicted to be involved in response to toxic substance. Located in cytoplasm and membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_003498.6

Inheritance

—

ClinVar variants

U:16B:2

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr16:11,668,455-11,679,152

External References & Databases

Ensembl (ENSG00000184602)

Transcript & Mutation Effects

hg38 • Region Span ~10.7 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 SNN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 17

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003498.6. 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				2 clinvar		2
missense			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	2	0	18

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003498.6	RefSeq	NP_003489.1	1	MANE Select
ENST00000329565.6	Ensembl	ENSP00000329287.5	1	MANE Select
ENST00000907333.1	Ensembl	ENSP00000577392.1	1	Standard
ENST00000907333.2	Ensembl	ENSP00000577392.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

response to toxic substance

Molecular Function

metal ion binding

Cellular Component

cytoplasm
mitochondrial outer membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329565
Coding exons: 1
Length: 10746
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125732
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.569	49	61.6	0.796	0.00000405	561
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0549