SND1

staphylococcal nuclease and tudor domain containing 1, the group of MicroRNA protein coding host genes|Tudor domain containing

Basic information

Region (hg38): 7:127652194-128092609

Links

ENSG00000197157NCBI:27044OMIM:602181HGNC:30646Uniprot:Q7KZF4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SND1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SND1 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
10
clinvar
4
clinvar
14
missense
41
clinvar
1
clinvar
42
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
1
1
2
non coding
26
clinvar
1
clinvar
4
clinvar
31
Total 0 0 68 12 9

Variants in SND1

This is a list of pathogenic ClinVar variants found in the SND1 region.

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

Position Type Phenotype Significance ClinVar
7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC Benign (Dec 31, 2019)718333
7-127652388-G-C Likely benign (Oct 23, 2018)726681
7-127652393-G-A not specified Uncertain significance (Dec 19, 2022)2337623
7-127652422-C-A not specified Uncertain significance (May 30, 2024)3321165
7-127652426-C-A not specified Uncertain significance (Dec 22, 2023)3166967
7-127686609-G-A Likely benign (Apr 11, 2018)770564
7-127686631-A-T SND1-related disorder Uncertain significance (Mar 25, 2024)3349057
7-127686636-T-A Likely benign (Aug 03, 2017)787863
7-127686653-G-A Teratoma Uncertain significance (Jan 01, 2023)2498252
7-127686663-T-A Likely benign (May 04, 2018)744005
7-127686728-C-T not specified Uncertain significance (May 04, 2022)2233924
7-127694891-A-G not specified Uncertain significance (Jun 18, 2021)2369361
7-127694893-G-A Likely benign (Dec 27, 2018)796889
7-127698952-A-C not specified Uncertain significance (Aug 15, 2023)2619108
7-127701159-C-T Benign (Dec 31, 2019)709901
7-127701188-T-G not specified Uncertain significance (Jan 19, 2024)3166966
7-127701240-G-A not specified Uncertain significance (Nov 08, 2022)2396048
7-127701242-T-G not specified Uncertain significance (May 01, 2022)2268588
7-127702457-C-T Likely benign (May 16, 2018)745295
7-127702504-C-T not specified Uncertain significance (Jun 06, 2023)2557976
7-127703235-T-A not specified Uncertain significance (Jan 06, 2023)2469919
7-127703300-A-G not specified Uncertain significance (Feb 21, 2024)3166968
7-127704846-A-G not specified Uncertain significance (Jan 25, 2023)2479172
7-127704856-G-A SND1-related disorder Likely benign (Jul 20, 2020)3052600
7-127704900-T-G not specified Uncertain significance (Jan 31, 2023)2478940

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SND1protein_codingprotein_codingENST00000354725 24440428
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9820.01791257310171257480.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.393345600.5960.00003385894
Missense in Polyphen84204.250.411271989
Synonymous1.481862140.8710.00001281824
Loss of Function5.721056.40.1770.00000337592

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005790.0000579
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.0001860.000185
European (Non-Finnish)0.00006170.0000615
Middle Eastern0.00005440.0000544
South Asian0.00009800.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Endonuclease that mediates miRNA decay of both protein- free and AGO2-loaded miRNAs (PubMed:28546213, PubMed:18453631). As part of its function in miRNA decay, regulates mRNAs involved in G1-to-S phase transition (PubMed:28546213). Functions as a bridging factor between STAT6 and the basal transcription factor (PubMed:12234934). Plays a role in PIM1 regulation of MYB activity (PubMed:9809063). Functions as a transcriptional coactivator for STAT5 (By similarity). {ECO:0000250|UniProtKB:Q78PY7, ECO:0000269|PubMed:12234934, ECO:0000269|PubMed:18453631, ECO:0000269|PubMed:28546213, ECO:0000269|PubMed:9809063}.;
Pathway
Viral carcinogenesis - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Disease;C-MYB transcription factor network;IL4;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction (Consensus)

Recessive Scores

pRec
0.127

Intolerance Scores

loftool
0.521
rvis_EVS
-1.06
rvis_percentile_EVS
7.48

Haploinsufficiency Scores

pHI
0.739
hipred
Y
hipred_score
0.774
ghis
0.587

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
K
gene_indispensability_pred
E
gene_indispensability_score
0.977

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Snd1
Phenotype

Gene ontology

Biological process
osteoblast differentiation;RNA catabolic process;regulation of cell cycle process;miRNA catabolic process;viral process;gene silencing by RNA;RNA phosphodiester bond hydrolysis, endonucleolytic;regulation of nucleic acid-templated transcription
Cellular component
nucleus;cytoplasm;cytosol;membrane;RISC complex;melanosome;extracellular exosome;dense body
Molecular function
transcription coregulator activity;RNA binding;nuclease activity;endonuclease activity;endoribonuclease activity;protein binding;cadherin binding;RISC complex binding