PREB

prolactin regulatory element binding, the group of WD repeat domain containing

Basic information

Region (hg38): 2:27130756-27134666

Links

ENSG00000138073 ∙ NCBI:10113 ∙ OMIM:606395 ∙ HGNC:9356 ∙ Uniprot:Q9HCU5 ∙ 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 PREB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PREB 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in PREB

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

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

Position	Type	Phenotype	Significance	ClinVar
2-27131436-C-T		not specified	Uncertain significance (Oct 26, 2021)
2-27131487-A-G		not specified	Uncertain significance (Sep 08, 2024)
2-27131674-C-T		not specified	Uncertain significance (Oct 19, 2024)
2-27131686-A-G		not specified	Uncertain significance (Mar 05, 2025)
2-27131758-C-A		not specified	Uncertain significance (Feb 08, 2025)
2-27131765-C-G		not specified	Uncertain significance (May 22, 2023)
2-27132237-C-T		not specified	Likely benign (Mar 08, 2025)
2-27132249-C-G		not specified	Uncertain significance (Apr 26, 2023)
2-27132249-C-T		not specified	Likely benign (Mar 29, 2022)
2-27132333-G-A		not specified	Uncertain significance (May 24, 2023)
2-27132380-G-C		not specified	Uncertain significance (Oct 01, 2024)
2-27132658-A-G		not specified	Uncertain significance (Jul 09, 2024)
2-27132696-G-A		not specified	Uncertain significance (Sep 01, 2021)
2-27132712-G-A		not specified	Likely benign (Jul 20, 2021)
2-27132714-C-A		not specified	Uncertain significance (Jan 22, 2024)
2-27132874-A-G		not specified	Uncertain significance (Aug 10, 2021)
2-27132889-G-T		not specified	Uncertain significance (Apr 15, 2024)
2-27132892-T-C		not specified	Uncertain significance (Feb 23, 2023)
2-27132911-C-T		not specified	Uncertain significance (Nov 13, 2024)
2-27132919-G-A		not specified	Uncertain significance (Feb 11, 2025)
2-27133122-A-G		not specified	Uncertain significance (Oct 25, 2024)
2-27133151-G-C		not specified	Uncertain significance (Jan 07, 2025)
2-27133268-G-C		not specified	Uncertain significance (Aug 11, 2022)
2-27133311-T-C		not specified	Uncertain significance (Feb 27, 2025)
2-27133570-T-C		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PREB	protein_coding	protein_coding	ENST00000260643	9	3920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000593	0.995	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.431	217	236	0.921	0.0000135	2657
Missense in Polyphen		72	86.013	0.83708		973
Synonymous	0.823	88	98.4	0.894	0.00000566	892
Loss of Function	2.48	9	21.4	0.421	0.00000115	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000261	0.000261
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.000653	0.000653
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor that specifically activates the small GTPase SAR1B. Mediates the recruitement of SAR1B and other COPII coat components to endoplasmic reticulum membranes and is therefore required for the formation of COPII transport vesicles from the ER. {ECO:0000250|UniProtKB:Q9WTV0, ECO:0000250|UniProtKB:Q9WUQ2}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);XBP1(S) activates chaperone genes;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.275

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.31

Haploinsufficiency Scores

• pHI: 0.294
• hipred: N
• hipred_score: 0.322
• ghis: 0.479

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.633

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Preb

Gene ontology

• Biological process: regulation of COPII vesicle coating;endoplasmic reticulum to Golgi vesicle-mediated transport;protein secretion;protein exit from endoplasmic reticulum;IRE1-mediated unfolded protein response;positive regulation of GTPase activity;COPII vesicle coating
• Cellular component: Golgi membrane;nucleus;endoplasmic reticulum membrane;membrane;integral component of endoplasmic reticulum membrane;endoplasmic reticulum exit site
• Molecular function: DNA binding;guanyl-nucleotide exchange factor activity;Sar guanyl-nucleotide exchange factor activity;GTPase activator activity;protein binding;GTPase binding