SNAI3

snail family transcriptional repressor 3, the group of Zinc fingers C2H2-type|SNAG transcriptional repressors

Basic information

Region (hg38): 16:88677688-88686507

Previous symbols: [ "ZNF293" ]

Links

ENSG00000185669

∙ NCBI:333929 ∙ OMIM:612741 ∙ HGNC:18411 ∙ Uniprot:Q3KNW1 ∙ 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 SNAI3 gene.

not_specified (54 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNAI3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178310.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			51 clinvar	3 clinvar		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNAI3	protein_coding	protein_coding	ENST00000332281	3	8812

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0132	0.873	125663	0	35	125698	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.866	229	195	1.17	0.0000131	1842
Missense in Polyphen		42	36.097	1.1635		279
Synonymous	-1.43	102	85.2	1.20	0.00000532	649
Loss of Function	1.31	4	7.99	0.501	4.26e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000243
Ashkenazi Jewish	0.000401	0.000397
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000129	0.000123
Middle Eastern	0.00	0.00
South Asian	0.000330	0.000327
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Seems to inhibit myoblast differentiation. Transcriptional repressor of E-box-dependent transactivation of downstream myogenic bHLHs genes. Binds preferentially to the canonical E-box sequences 5'-CAGGTG-3' and 5'-CACCTG-3' (By similarity). {ECO:0000250}.;
Pathway: downregulated of mta-3 in er-negative breast tumors (Consensus)

Recessive Scores

pRec: 0.128

Intolerance Scores

loftool: 0.646
rvis_EVS: 0.96
rvis_percentile_EVS: 90.11

Haploinsufficiency Scores

pHI: 0.101
hipred: N
hipred_score: 0.180
ghis: 0.447

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.857

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Snai3
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; hematopoietic system phenotype; vision/eye phenotype; immune system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated
Cellular component: nucleus;transcription factor complex
Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;copper ion binding