PEF1

penta-EF-hand domain containing 1, the group of EF-hand domain containing

Basic information

Region (hg38): 1:31629866-31644896

Links

ENSG00000162517 ∙ NCBI:553115 ∙ OMIM:610033 ∙ HGNC:30009 ∙ Uniprot:Q9UBV8 ∙ 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 PEF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEF1 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in PEF1

This is a list of pathogenic ClinVar variants found in the PEF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-31630634-C-A		not specified	Uncertain significance (Nov 25, 2024)
1-31630639-T-C		not specified	Uncertain significance (Aug 30, 2021)
1-31630680-G-T		not specified	Uncertain significance (Nov 15, 2021)
1-31630695-C-T		not specified	Uncertain significance (Jul 06, 2021)
1-31630756-T-C		not specified	Uncertain significance (Nov 27, 2023)
1-31630774-G-A		not specified	Uncertain significance (May 23, 2023)
1-31630785-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-31632519-T-C		not specified	Uncertain significance (Nov 13, 2023)
1-31632536-C-T		not specified	Uncertain significance (Nov 13, 2024)
1-31632561-T-C		not specified	Uncertain significance (Jul 28, 2024)
1-31632599-T-C		not specified	Uncertain significance (Feb 22, 2023)
1-31632611-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-31633200-T-C		not specified	Uncertain significance (Dec 11, 2023)
1-31633221-T-C		not specified	Uncertain significance (Jan 12, 2024)
1-31633242-T-C		not specified	Uncertain significance (Nov 01, 2022)
1-31633257-G-A		not specified	Uncertain significance (Jan 02, 2024)
1-31633268-C-A		not specified	Uncertain significance (Sep 16, 2021)
1-31633306-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-31635306-A-G		not specified	Uncertain significance (Jul 09, 2024)
1-31635356-T-A		not specified	Uncertain significance (Mar 08, 2024)
1-31635381-C-T		not specified	Uncertain significance (Dec 12, 2023)
1-31635417-C-T		not specified	Uncertain significance (Nov 13, 2024)
1-31635423-G-C		not specified	Uncertain significance (Mar 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEF1	protein_coding	protein_coding	ENST00000373703	5	15035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000151	0.879	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.284	156	166	0.938	0.00000922	1812
Missense in Polyphen		38	54.631	0.69557		650
Synonymous	-0.315	68	64.8	1.05	0.00000363	584
Loss of Function	1.41	8	13.6	0.587	5.83e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000873	0.0000873
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-binding protein that acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium. Together with PDCD6, acts as calcium-dependent adapter for the BCR(KLHL12) complex, a complex involved in endoplasmic reticulum (ER)-Golgi transport by regulating the size of COPII coats (PubMed:27716508). In response to cytosolic calcium increase, the heterodimer formed with PDCD6 interacts with, and bridges together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export, which is required for neural crest specification (PubMed:27716508). Its role in the heterodimer formed with PDCD6 is however unclear: some evidences show that PEF1 and PDCD6 work together and promote association between PDCD6 and SEC31 in presence of calcium (PubMed:27716508). Other reports show that PEF1 dissociates from PDCD6 in presence of calcium, and may act as a negative regulator of PDCD6 (PubMed:11278427). Also acts as a negative regulator of ER-Golgi transport; possibly by inhibiting interaction between PDCD6 and SEC31 (By similarity). {ECO:0000250|UniProtKB:Q641Z8, ECO:0000269|PubMed:11278427, ECO:0000269|PubMed:27716508}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.361
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.239
• hipred: N
• hipred_score: 0.440
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pef1

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;neural crest formation;neural crest cell development;COPII vesicle coating;response to calcium ion;positive regulation of protein monoubiquitination
• Cellular component: Golgi membrane;cytoplasm;endoplasmic reticulum;COPII vesicle coat;Cul3-RING ubiquitin ligase complex;extracellular exosome
• Molecular function: RNA binding;calcium ion binding;protein binding;protein heterodimerization activity;protein dimerization activity;calcium-dependent protein binding;molecular adaptor activity