SND1

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

Basic information

Region (hg38): 7:127652193-128092609

Links

ENSG00000197157 ∙ NCBI:27044 ∙ OMIM:602181 ∙ HGNC:30646 ∙ Uniprot:Q7KZF4 ∙ 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 SND1 gene.

• Inborn genetic diseases (44 variants)
• not provided (26 variants)
• Hypospadias (1 variants)

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				9	4	13
missense			29	1		30
nonsense			1			1
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			19	1	4	24
Total	0	0	49	11	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)
7-127652388-G-C			Likely benign (Oct 23, 2018)
7-127652393-G-A		not specified	Uncertain significance (Dec 19, 2022)
7-127652426-C-A		not specified	Uncertain significance (Dec 22, 2023)
7-127686609-G-A			Likely benign (Apr 11, 2018)
7-127686636-T-A			Likely benign (Aug 03, 2017)
7-127686653-G-A		Teratoma	Uncertain significance (Jan 01, 2023)
7-127686663-T-A			Likely benign (May 04, 2018)
7-127686728-C-T		not specified	Uncertain significance (May 04, 2022)
7-127694891-A-G		not specified	Uncertain significance (Jun 18, 2021)
7-127694893-G-A			Likely benign (Dec 27, 2018)
7-127698952-A-C		not specified	Uncertain significance (Aug 15, 2023)
7-127701159-C-T			Benign (Dec 31, 2019)
7-127701188-T-G		not specified	Uncertain significance (Jan 19, 2024)
7-127701240-G-A		not specified	Uncertain significance (Nov 08, 2022)
7-127701242-T-G		not specified	Uncertain significance (May 01, 2022)
7-127702457-C-T			Likely benign (May 16, 2018)
7-127702504-C-T		not specified	Uncertain significance (Jun 06, 2023)
7-127703235-T-A		not specified	Uncertain significance (Jan 06, 2023)
7-127703300-A-G		not specified	Uncertain significance (Feb 21, 2024)
7-127704846-A-G		not specified	Uncertain significance (Jan 25, 2023)
7-127704856-G-A		SND1-related disorder	Likely benign (Jul 20, 2020)
7-127704900-T-G		not specified	Uncertain significance (Jan 31, 2023)
7-127704914-C-T		not specified	Uncertain significance (Dec 14, 2023)
7-127704919-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SND1	protein_coding	protein_coding	ENST00000354725	24	440428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0179	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.39	334	560	0.596	0.0000338	5894
Missense in Polyphen		84	204.25	0.41127		1989
Synonymous	1.48	186	214	0.871	0.0000128	1824
Loss of Function	5.72	10	56.4	0.177	0.00000337	592

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000186	0.000185
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

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

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

Mouse Genome Informatics

• Gene name: Snd1

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