SND1

protein-coding

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

Gene summary

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]

MANE transcript

NM_014390.4

Inheritance

—

ClinVar variants

U:120B:17

Top phenotype

SND1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr7:127,652,194-128,092,609

External References & Databases

Ensembl (ENSG00000197157)

Transcript & Mutation Effects

hg38 • Region Span ~440.4 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 SND1 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 170

not providedTotal: 27

SND1-related disorderTotal: 4

TeratomaTotal: 1

HypospadiasTotal: 1

Long QT syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014390.4. 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			1 clinvar	11 clinvar	4 clinvar	16
missense			107 clinvar	2 clinvar		109
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	120	13	4	137

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014390.4	RefSeq	NP_055205.2	24	MANE Select
ENST00000354725.8	Ensembl	ENSP00000346762.3	24	MANE Select
ENST00000486037.1	Ensembl	ENSP00000419327.1	6	Standard
ENST00000903601.1	Ensembl	ENSP00000573660.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Viral carcinogenesis - Homo sapiens (human)
Epstein-Barr virus infection - Homo sapiens (human)
Disease
C-MYB transcription factor network
IL4

Biological Process

osteoblast differentiation
RNA catabolic process
regulation of cell cycle process
miRNA catabolic process
viral process

Molecular Function

transcription coregulator activity
RNA binding
nuclease activity
endonuclease activity
endoribonuclease activity

Cellular Component

nucleus
cytoplasm
cytosol
membrane
RISC complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000354725
Coding exons: 24
Length: 440428
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125748
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.39	334	560	0.596	0.0000338	5894
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.521
RVIS EVS: -1.06
RVIS percentile EVS: 7.48

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.977

Gene Damage Prediction

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