SCRT1

protein-coding

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

Gene summary

This gene encodes a C2H2-type zinc finger transcriptional repressor that binds to E-box motifs. The encoded protein may promote neural differention and may be involved in cancers with neuroendocrine features. [provided by RefSeq, Jul 2013]

MANE transcript

NM_031309.6

Inheritance

—

ClinVar variants

U:38B:2

Top phenotype

—

Max pathogenic AF

—

Genomic locus

chr8:144,330,565-144,336,482

External References & Databases

Ensembl (ENSG00000261678)

Transcript & Mutation Effects

hg38 • Region Span ~5.9 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 SCRT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031309.6. 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				2 clinvar		2
missense			38 clinvar			38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	2	0	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031309.6	RefSeq	NP_112599.2	2	MANE Select
ENST00000569446.3	Ensembl	ENSP00000455711.1	2	MANE Select
ENST00001136680.1	Ensembl	ENSP00000814185.1	2	Standard
XM_024447291.2	RefSeq	XP_024303059.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
regulation of transcription, DNA-templated
regulation of neuron migration

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

Cellular Component

nucleus
nuclear body

dbNSFP Gene Annotations

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}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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