SCRT2

scratch family transcriptional repressor 2, the group of Zinc fingers C2H2-type|SNAG transcriptional repressors

Basic information

Region (hg38): 20:661596-675802

Links

ENSG00000215397 ∙ NCBI:85508 ∙ ∙ HGNC:15952 ∙ Uniprot:Q9NQ03 ∙ 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 SCRT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCRT2 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			28	3		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in SCRT2

This is a list of pathogenic ClinVar variants found in the SCRT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-663693-G-T		not specified	Uncertain significance (Apr 09, 2024)
20-663700-G-T		not specified	Uncertain significance (Apr 30, 2024)
20-663715-C-T		not specified	Uncertain significance (Feb 01, 2025)
20-663754-A-G		not specified	Uncertain significance (Aug 10, 2024)
20-663779-C-G		not specified	Uncertain significance (Aug 10, 2021)
20-663809-G-C		not specified	Uncertain significance (Jun 07, 2024)
20-663820-T-C		not specified	Uncertain significance (Jan 23, 2025)
20-663952-C-A		not specified	Uncertain significance (Sep 14, 2023)
20-663982-G-C		not specified	Likely benign (Apr 07, 2023)
20-664152-T-G		not specified	Likely benign (Apr 07, 2023)
20-664161-G-T		not specified	Uncertain significance (Nov 02, 2023)
20-664177-C-T		not specified	Uncertain significance (Feb 18, 2025)
20-664182-G-C		not specified	Uncertain significance (Apr 07, 2023)
20-664183-C-G		not specified	Uncertain significance (Oct 06, 2021)
20-664185-C-T		not specified	Uncertain significance (Oct 19, 2024)
20-664186-C-T		not specified	Uncertain significance (Apr 07, 2023)
20-664188-C-G		not specified	Uncertain significance (Apr 22, 2024)
20-664200-G-A		not specified	Uncertain significance (Sep 27, 2021)
20-664201-A-C		not specified	Likely benign (Apr 07, 2023)
20-664219-C-T		not specified	Uncertain significance (Aug 01, 2024)
20-664243-A-C		not specified	Uncertain significance (Sep 27, 2021)
20-664287-G-T		not specified	Uncertain significance (Nov 14, 2024)
20-664305-C-T		not specified	Uncertain significance (Dec 18, 2023)
20-664314-C-A		not specified	Uncertain significance (Dec 03, 2024)
20-664375-G-A		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCRT2	protein_coding	protein_coding	ENST00000246104	2	14584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.910	0.0893	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.59	78	174	0.448	0.0000121	1901
Missense in Polyphen		33	82.843	0.39834		809
Synonymous	1.67	69	89.1	0.775	0.00000711	644
Loss of Function	2.58	0	7.76	0.00	3.78e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Recessive Scores

• pRec: 0.161

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.651
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.651

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scrt2

Zebrafish Information Network

• Gene name: scrt2
• Affected structure: primary neuron
• Phenotype tag: abnormal
• Phenotype quality: proliferative

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;regulation of neuron migration
• Cellular component: nuclear chromatin;nucleus
• 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;metal ion binding;E-box binding