CREB3L1

protein-coding

cAMP responsive element binding protein 3 like 1, the group of CREB3 transcription factor family

Gene summary

The protein encoded by this gene is normally found in the membrane of the endoplasmic reticulum (ER). However, upon stress to the ER, the encoded protein is cleaved and the released cytoplasmic transcription factor domain translocates to the nucleus. There it activates the transcription of target genes by binding to box-B elements. [provided by RefSeq, Jun 2013]

MANE transcript

NM_052854.4

Inheritance

AR, AD

ClinVar variants

P:16U:148B:118

Top phenotype

Osteogenesis imperfecta, type XVI

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr11:46,277,662-46,321,409

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~43.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

osteogenesis imperfecta type 16STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014544

Submitter: Labcorp Genetics (formerly Invitae)

osteogenesis imperfecta type 3SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0009804

Submitter: Orphanet

osteogenesis imperfecta type 16MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0014544

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Osteogenesis imperfecta, type XVIAR

Manifestation: Musculoskeletal

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 24079343; 30657919Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CREB3L1 variants in ClinVar

9 Conditions Cataloged
not providedTotal: 263
Inborn genetic diseasesTotal: 88
not specifiedTotal: 39
Osteogenesis imperfecta type 16Total: 26
CREB3L1-related disorderTotal: 17
TeratomaTotal: 1
CREB3L1-related disordersTotal: 1
Osteogenesis imperfectaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052854.4. 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
96
clinvar
4
clinvar
103
missense
1
clinvar
143
clinvar
14
clinvar
3
clinvar
161
nonsense
4
clinvar
1
clinvar
1
clinvar
6
start loss
0
frameshift
4
clinvar
3
clinvar
1
clinvar
8
splice donor/acceptor (+/-2bp)
3
clinvar
1
clinvar
4
Total971481108282

Highest pathogenic variant AF is 0.000006570993

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_052854.4RefSeqNP_443086.112MANE Select
ENST00000621158.5EnsemblENSP00000481956.112MANE Select
NM_001425266.1RefSeqNP_001412195.112Standard
NM_001425267.1RefSeqNP_001412196.112Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • PI3K-Akt signaling pathway - Homo sapiens (human)
  • Cortisol synthesis and secretion - Homo sapiens (human)
  • Relaxin signaling pathway - Homo sapiens (human)
  • Aldosterone synthesis and secretion - Homo sapiens (human)
  • Dopaminergic synapse - Homo sapiens (human)

Biological Process

  • negative regulation of transcription by RNA polymerase II
  • osteoblast differentiation
  • multicellular organism development
  • negative regulation of gene expression
  • endoplasmic reticulum unfolded protein response

Molecular Function

  • DNA-binding transcription factor activity, RNA polymerase II-specific
  • DNA-binding transcription repressor activity, RNA polymerase II-specific
  • DNA-binding transcription activator activity, RNA polymerase II-specific
  • chromatin binding
  • protein binding

Cellular Component

  • nuclear chromatin
  • nucleus
  • endoplasmic reticulum
  • endoplasmic reticulum membrane
  • membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000529193
Coding exons
12
Length
43761
Individuals with no LoFs
124639
Homozygous LoFs
0
Heterozygous LoFs
6
Defined
124645
p
0.0000241
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.9492432880.8430.00001643322
Missense (PolyPhen)7296.250.748051173
Synonymous0.9621171310.8930.000008811019
Loss of Function3.90221.50.09290.00000107260

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000650.000065rare
Latino/Admixed American0.0000300.000029rare
Ashkenazi Jewish00.0absent
East Asian0.0000560.000056rare
Finnish00.0absent
European (Non-Finnish)0.0000360.000027rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Transcription factor involved in unfolded protein response (UPR). Binds the DNA consensus sequence 5'-GTGXGCXGC-3' (PubMed:21767813). In the absence of endoplasmic reticulum (ER) stress, inserted into ER membranes, with N-terminal DNA-binding and transcription activation domains oriented toward the cytosolic face of the membrane. In response to ER stress, transported to the Golgi, where it is cleaved in a site-specific manner by resident proteases S1P/MBTPS1 and S2P/MBTPS2. The released N-terminal cytosolic domain is translocated to the nucleus to effect transcription of specific target genes. Plays a critical role in bone formation through the transcription of COL1A1, and possibly COL1A2, and the secretion of bone matrix proteins. Directly binds to the UPR element (UPRE)-like sequence in an osteoblast-specific COL1A1 promoter region and induces its transcription. Does not regulate COL1A1 in other tissues, such as skin (By similarity). Required to protect astrocytes from ER stress-induced cell death. In astrocytes, binds to the cAMP response element (CRE) of the BiP/HSPA5 promoter and participate in its transcriptional activation (By similarity). Required for TGFB1 to activate genes involved in the assembly of collagen extracellular matrix (PubMed:25310401). {ECO:0000250|UniProtKB:Q9Z125, ECO:0000269|PubMed:12054625, ECO:0000269|PubMed:21767813, ECO:0000269|PubMed:25310401}.;
Disease
DISEASE: Osteogenesis imperfecta 16 (OI16) [MIM:616229]: An autosomal recessive form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI16 is a severe form. {ECO:0000269|PubMed:24079343}. Note=The disease may be caused by mutations affecting the gene represented in this entry. OI16 affected patients show a genomic deletion encompassing CREB3L1 and the first exon of DGKZ. The absence of this exon does not affect all DGKZ isoforms, some are still produced at normal level. It cannot be ruled out that DGKZ could contribute to the phenotype, but in view of its role in bone formation, CREB3L1 is a strong OI16-causing candidate (PubMed:24079343). This hypothesis is corroborated by the observation of CREB3L1 knockout mice which exhibit features reminiscent of severe human osteogenesis imperfecta. {ECO:0000269|PubMed:24079343}.;

Recessive Scores

pRec
0.138

Intolerance Scores

RVIS EVS
0.29
RVIS percentile EVS
71.5

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Indispensability pred.
E
Indispensability score
0.721

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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