TRERF1

transcriptional regulating factor 1, the group of Myb/SANT domain containing

Basic information

Region (hg38): 6:42224930-42452051

Previous symbols: [ "BCAR2" ]

Links

ENSG00000124496 ∙ NCBI:55809 ∙ OMIM:610322 ∙ HGNC:18273 ∙ Uniprot:Q96PN7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRERF1 gene.

• Inborn genetic diseases (38 variants)
• not provided (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRERF1 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				4	7	11
missense			36	3	5	44
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	37	7	13

Variants in TRERF1

This is a list of pathogenic ClinVar variants found in the TRERF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-42228356-C-T		not specified	Likely benign (Feb 28, 2023)
6-42228388-T-C		not specified	Uncertain significance (Sep 22, 2023)
6-42228401-C-T		not specified	Uncertain significance (Dec 14, 2021)
6-42228404-T-G		not specified	Uncertain significance (Nov 29, 2023)
6-42228422-C-G		not specified	Uncertain significance (May 26, 2022)
6-42228452-C-T		not specified	Uncertain significance (Aug 06, 2021)
6-42228523-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-42228534-G-C			Likely benign (May 01, 2023)
6-42228607-T-C		not specified	Uncertain significance (Feb 28, 2023)
6-42232727-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-42232757-T-G		not specified	Uncertain significance (Sep 01, 2021)
6-42232836-G-C		not specified	Uncertain significance (Jan 03, 2024)
6-42236244-G-A			Benign (May 24, 2018)
6-42236246-G-T		not specified	Uncertain significance (Feb 13, 2024)
6-42236269-G-A		not specified	Uncertain significance (May 18, 2022)
6-42236270-GC-G			Uncertain significance (Jun 07, 2017)
6-42236277-C-T			Likely benign (May 01, 2023)
6-42236297-C-T		not specified	Uncertain significance (Dec 20, 2022)
6-42243301-G-A		not specified	Uncertain significance (Jan 16, 2024)
6-42246484-C-T		not specified	Uncertain significance (Oct 25, 2023)
6-42246553-A-C			Benign (Dec 31, 2019)
6-42254901-C-T		not specified	Uncertain significance (Jul 19, 2023)
6-42256785-T-G			Benign (Dec 31, 2019)
6-42256794-C-A		not specified	Uncertain significance (Jul 26, 2022)
6-42257025-T-G		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRERF1	protein_coding	protein_coding	ENST00000372922	14	227121

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.15e-8	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	535	703	0.761	0.0000426	7810
Missense in Polyphen		58	90.67	0.63969		1002
Synonymous	0.0172	305	305	0.999	0.0000208	2401
Loss of Function	6.64	2	55.2	0.0362	0.00000292	564

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds DNA and activates transcription of CYP11A1. Interaction with CREBBP and EP300 results in a synergistic transcriptional activation of CYP11A1. {ECO:0000269|PubMed:11349124, ECO:0000269|PubMed:16371131}.
• Pathway: Mesodermal Commitment Pathway (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.0508
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.38

Haploinsufficiency Scores

• pHI: 0.811
• hipred: Y
• hipred_score: 0.670
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.705

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trerf1

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;steroid biosynthetic process;cholesterol catabolic process;multicellular organism development;homeostatic process;positive regulation of transcription, DNA-templated;regulation of hormone biosynthetic process
• Cellular component: histone deacetylase complex;nucleus;nucleoplasm;transcription factor complex;nucleolus;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription coregulator activity;transcription factor binding;DNA binding, bending;nuclear receptor transcription coactivator activity;transcription regulatory region DNA binding;metal ion binding