GRPEL1

GrpE like 1, mitochondrial, the group of TIM23 complex

Basic information

Region (hg38): 4:7058671-7068085

Links

ENSG00000109519 ∙ NCBI:80273 ∙ OMIM:606173 ∙ HGNC:19696 ∙ Uniprot:Q9HAV7 ∙ 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 GRPEL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRPEL1 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in GRPEL1

This is a list of pathogenic ClinVar variants found in the GRPEL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-7060926-A-G		not specified	Uncertain significance (Jun 30, 2022)
4-7061063-G-C		not specified	Uncertain significance (Jun 23, 2021)
4-7061094-T-C		not specified	Uncertain significance (May 05, 2023)
4-7061110-G-A		not specified	Uncertain significance (Mar 25, 2024)
4-7061112-G-C		not specified	Uncertain significance (Oct 17, 2023)
4-7061119-C-T		not specified	Uncertain significance (Aug 12, 2022)
4-7061144-A-C		not specified	Uncertain significance (Oct 05, 2023)
4-7061151-G-T		not specified	Uncertain significance (Sep 01, 2021)
4-7061167-C-T			Likely benign (Mar 01, 2023)
4-7062427-G-A		not specified	Uncertain significance (Dec 09, 2023)
4-7062460-A-G		not specified	Uncertain significance (Mar 01, 2023)
4-7064104-A-G		not specified	Uncertain significance (Apr 08, 2024)
4-7064137-T-C		not specified	Uncertain significance (Aug 15, 2023)
4-7064167-A-G		not specified	Uncertain significance (Jan 10, 2023)
4-7064194-G-A		not specified	Uncertain significance (Sep 26, 2023)
4-7068007-G-A		not specified	Uncertain significance (Jan 03, 2024)
4-7068026-C-G		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRPEL1	protein_coding	protein_coding	ENST00000264954	4	9292

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.139	0.843	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00573	122	122	1.00	0.00000649	1410
Missense in Polyphen		33	44.558	0.7406		496
Synonymous	0.139	49	50.3	0.975	0.00000266	424
Loss of Function	2.04	3	9.96	0.301	5.17e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000643	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000548	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner (By similarity). Seems to control the nucleotide-dependent binding of mitochondrial HSP70 to substrate proteins (PubMed:11311562). {ECO:0000250|UniProtKB:P38523, ECO:0000269|PubMed:11311562}.
• Pathway: Metabolism of proteins;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.165
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• pHI: 0.196
• hipred: Y
• hipred_score: 0.783
• ghis: 0.455

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grpel1

Gene ontology

• Biological process: protein folding;protein import into mitochondrial matrix;regulation of catalytic activity
• Cellular component: PAM complex, Tim23 associated import motor;nucleus;mitochondrion;mitochondrial matrix
• Molecular function: adenyl-nucleotide exchange factor activity;protein homodimerization activity;unfolded protein binding;chaperone binding