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.

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.

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						0
missense			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in SNAI3

This is a list of pathogenic ClinVar variants found in the SNAI3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-88681190-G-A		not specified	Uncertain significance (Mar 01, 2023)
16-88681228-C-A		not specified	Uncertain significance (Dec 22, 2023)
16-88681229-A-T		not specified	Uncertain significance (May 25, 2022)
16-88681247-C-G		not specified	Uncertain significance (Jun 11, 2021)
16-88681339-C-A		not specified	Uncertain significance (Jan 03, 2024)
16-88681351-C-T		not specified	Uncertain significance (May 13, 2024)
16-88681358-T-C		not specified	Uncertain significance (Mar 01, 2023)
16-88681391-C-A		not specified	Uncertain significance (Jan 03, 2024)
16-88681414-G-A		not specified	Uncertain significance (Sep 21, 2023)
16-88681450-A-G		not specified	Uncertain significance (Sep 26, 2023)
16-88681459-T-A		not specified	Uncertain significance (Aug 12, 2021)
16-88681495-C-T		not specified	Uncertain significance (Aug 02, 2021)
16-88681505-G-A		not specified	Likely benign (Aug 08, 2023)
16-88681511-C-T		not specified	Uncertain significance (Aug 14, 2023)
16-88681514-C-T		not specified	Uncertain significance (Dec 03, 2021)
16-88681523-C-A		not specified	Uncertain significance (Oct 18, 2021)
16-88681559-C-T		not specified	Uncertain significance (Mar 13, 2023)
16-88681568-G-A		not specified	Uncertain significance (Dec 17, 2023)
16-88681591-C-A		not specified	Uncertain significance (Mar 25, 2024)
16-88681609-C-T		not specified	Uncertain significance (Mar 06, 2023)
16-88681628-G-T		not specified	Uncertain significance (Nov 21, 2022)
16-88681660-C-T		not specified	Likely benign (Aug 22, 2023)
16-88681708-T-C		not specified	Uncertain significance (Apr 23, 2024)
16-88686333-C-G		not specified	Uncertain significance (Jun 24, 2022)
16-88686337-G-C		not specified	Uncertain significance (Jul 25, 2023)

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