TRERF1

protein-coding

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

Gene summary

This gene encodes a zinc-finger transcriptional regulating protein which interacts with CBP/p300 to regulate the human gene CYP11A1. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]

Previous symbols:

BCAR2

MANE transcript

NM_001395490.1

Inheritance

ClinVar variants

U:170B:25

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr6:42,224,931-42,452,051

External References & Databases

Ensembl (ENSG00000124496)

Transcript & Mutation Effects

hg38 • Region Span ~227.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRERF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 161

not providedTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395490.1. 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	5 clinvar	7 clinvar	14
missense			163 clinvar	8 clinvar	5 clinvar	176
nonsense						0
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	170	13	12	195

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 151 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395490.1	RefSeq	NP_001382419.1	14	MANE Select
ENST00000695948.1	Ensembl	ENSP00000512293.1	14	MANE Select
NM_001297573.2	RefSeq	NP_001284502.1	14	Standard
NM_001391983.1	RefSeq	NP_001378912.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mesodermal Commitment Pathway

Biological Process

regulation of transcription by RNA polymerase II
steroid biosynthetic process
cholesterol catabolic process
multicellular organism development
homeostatic process

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

Cellular Component

histone deacetylase complex
nucleus
nucleoplasm
transcription factor complex
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372922
Coding exons: 14
Length: 227121
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.26	535	703	0.761	0.0000426	7810
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.162

Intolerance Scores

LoFtool: 0.0508
RVIS EVS: 0.75
RVIS percentile EVS: 86.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.705

Gene Damage Prediction

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