SCRT1

scratch family transcriptional repressor 1, the group of SNAG transcriptional repressors|Zinc fingers C2H2-type

Basic information

Region (hg38): 8:144330565-144336482

Links

ENSG00000261678 ∙ NCBI:83482 ∙ OMIM:605858 ∙ HGNC:15950 ∙ Uniprot:Q9BWW7 ∙ 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 SCRT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCRT1 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				1		1
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in SCRT1

This is a list of pathogenic ClinVar variants found in the SCRT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144333205-G-C		not specified	Uncertain significance (Dec 20, 2023)
8-144333274-T-A		not specified	Uncertain significance (Dec 06, 2023)
8-144333333-G-A		not specified	Uncertain significance (Dec 19, 2022)
8-144333679-C-T		not specified	Uncertain significance (Jan 05, 2022)
8-144333696-C-T		not specified	Uncertain significance (Jan 24, 2024)
8-144333772-C-G		not specified	Uncertain significance (May 31, 2023)
8-144333810-G-A		not specified	Uncertain significance (Sep 22, 2023)
8-144333873-G-A		not specified	Uncertain significance (Sep 29, 2022)
8-144333892-C-T		not specified	Uncertain significance (Jan 03, 2024)
8-144333966-G-A		not specified	Uncertain significance (Oct 25, 2023)
8-144334001-C-T			Likely benign (Jan 01, 2023)
8-144334028-C-G		not specified	Uncertain significance (Jul 26, 2022)
8-144334084-C-T		not specified	Uncertain significance (Feb 06, 2023)
8-144334111-G-T		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that binds E-box motif CAGGTG. Can modulate the action of basic helix-loop-helix (bHLH) transcription factors, critical for neuronal differentiation. {ECO:0000269|PubMed:11274425}.

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.367
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scrt1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;regulation of neuron migration
• Cellular component: nucleus;nuclear body
• Molecular function: RNA polymerase II regulatory region 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;sequence-specific DNA binding;metal ion binding