SND1

Chr 7

staphylococcal nuclease and tudor domain containing 1

Also known as: TDRD11, TSN, Tudor-SN, p100

NCBI Gene: 27044ENSG00000197157UniProt: Q7KZF4

This gene encodes a transcriptional co-activator that interacts with the acidic domain of Epstein-Barr virus nuclear antigen 2 (EBNA 2), a transcriptional activator that is required for B-lymphocyte transformation. Other transcription factors that interact with this protein are signal transducers and activators of transcription, STATs. This protein is also thought to be essential for normal cell growth. A similar protein in mammals and other organisms is a component of the RNA-induced silencing complex (RISC). [provided by RefSeq, Jul 2016]

236
ClinVar variants
25
Pathogenic / LP
0.98
pLI score· haploinsufficient
0
Active trials
Clinical Summary— SND1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
25 Pathogenic / Likely Pathogenic· 184 VUS of 236 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.30LOEUF
pLI 0.982
Z-score 5.72
OE 0.18 (0.11–0.30)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
3.39Z-score
OE missense 0.60 (0.54–0.65)
334 obs / 560.0 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.18 (0.11–0.30)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.60 (0.54–0.65)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.87
0≤1.21.6
LoF obs/exp: 10 / 56.4Missense obs/exp: 334 / 560.0Syn Z: 1.48

ClinVar Variant Classifications

236 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic24
Likely Pathogenic1
VUS184
Likely Benign17
Benign10
24
Pathogenic
1
Likely Pathogenic
184
VUS
17
Likely Benign
10
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
24
0
24
Likely Pathogenic
0
0
1
0
1
VUS
1
169
14
0
184
Likely Benign
0
4
2
11
17
Benign
0
0
2
8
10
Total11734319236

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SND1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Integrated proteogenomic characterization of urothelial carcinoma of the bladder.
Xu N et al.·J Hematol Oncol
2022
The palmitoylation of AEG-1 dynamically modulates the progression of hepatocellular carcinoma.
Zhou B et al.·Theranostics
2022
Oncoprotein SND1-enriched exosomes facilitate melanoma lung metastasis by regulating CD47-SIRPα-mediated macrophage reprogramming.
Chen Y et al.·Cancer Lett
2025
[Identification and Analysis of SND1 as an Oncogene and Prognostic Biomarker 
for Lung Adenocarcinoma].
Zhang R et al.·Zhongguo Fei Ai Za Zhi
2024
The chromatin architectural regulator SND1 mediates metastasis in triple-negative breast cancer by promoting CDH1 gene methylation.
Zhang H et al.·Breast Cancer Res
2023
SND1 expression in breast cancer tumors is associated with poor prognosis.
Gu X et al.·Ann N Y Acad Sci
2018
Correlated overexpression of metadherin and SND1 in glioma cells.
Tong L et al.·Biol Chem
2016
Pediatric pancreatic acinar cell carcinoma with a non-canonical BRAF-KMT2C fusion and a classic SND1-BRAF fusion: a case report and literature review.
Wang Y et al.·BMC Pediatr
2025Review
SND1 facilitates the invasion and migration of cervical cancer cells by Smurf1-mediated degradation of FOXA2.
Zhan F et al.·Exp Cell Res
2020
SPT6 recruits SND1 to co-activate human telomerase reverse transcriptase to promote colon cancer progression.
Diao C et al.·Mol Oncol
2021
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools