GRPEL2

GrpE like 2, mitochondrial

Basic information

Region (hg38): 5:149345429-149354583

Links

ENSG00000164284 ∙ NCBI:134266 ∙ OMIM:618545 ∙ HGNC:21060 ∙ Uniprot:Q8TAA5 ∙ 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 GRPEL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRPEL2 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			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in GRPEL2

This is a list of pathogenic ClinVar variants found in the GRPEL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-149345562-C-T		not specified	Uncertain significance (Jun 24, 2022)
5-149345583-G-A		not specified	Uncertain significance (Jan 23, 2023)
5-149345606-T-C		not specified	Uncertain significance (Jun 29, 2022)
5-149348280-C-T		not specified	Likely benign (Feb 16, 2023)
5-149348328-G-A		not specified	Uncertain significance (Oct 20, 2023)
5-149348357-C-G		not specified	Uncertain significance (Aug 08, 2022)
5-149348375-G-A		not specified	Uncertain significance (Sep 16, 2021)
5-149348393-G-A		not specified	Likely benign (Aug 08, 2022)
5-149349667-G-A		not specified	Uncertain significance (Dec 11, 2023)
5-149349694-G-A		not specified	Uncertain significance (Dec 14, 2021)
5-149350928-T-G		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRPEL2	protein_coding	protein_coding	ENST00000329271	4	9154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000359	0.844	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.362	112	123	0.908	0.00000631	1438
Missense in Polyphen		24	42.437	0.56555		556
Synonymous	0.698	43	49.2	0.873	0.00000251	465
Loss of Function	1.26	7	11.7	0.600	7.62e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000341	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000976	0.0000967
Middle Eastern	0.000341	0.000326
South Asian	0.0000327	0.0000327
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. Seems to control the nucleotide-dependent binding of mitochondrial HSP70 to substrate proteins. Stimulates ATPase activity of mt-HSP70. May also serve to modulate the interconversion of oligomeric (inactive) and monomeric (active) forms of mt-HSP70 (By similarity). {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Metabolism of proteins;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.0810

Intolerance Scores

• loftool: 0.425
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.0285
• hipred: Y
• hipred_score: 0.513
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.839

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grpel2

Gene ontology

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