IMMP2L

inner mitochondrial membrane peptidase subunit 2

Basic information

Region (hg38): 7:110662643-111562517

Previous symbols: [ "IMMP2L-IT1" ]

Links

ENSG00000184903 ∙ NCBI:83943 ∙ OMIM:605977 ∙ HGNC:14598 ∙ Uniprot:Q96T52 ∙ 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 IMMP2L gene.

• Inborn genetic diseases (31 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IMMP2L 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					2	2
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			23		4	27
Total	0	0	31	1	6

Variants in IMMP2L

This is a list of pathogenic ClinVar variants found in the IMMP2L region.

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

Position	Type	Phenotype	Significance	ClinVar
7-110663646-C-G		not specified	Uncertain significance (Mar 24, 2023)
7-110663677-C-A		not specified	Uncertain significance (Jan 08, 2024)
7-110886634-C-A		not specified	Uncertain significance (Dec 07, 2021)
7-110886648-A-G		not specified	Uncertain significance (Feb 06, 2023)
7-110886657-C-T		not specified	Uncertain significance (Aug 26, 2022)
7-110886658-G-A			Likely benign (Jul 31, 2018)
7-110886666-T-C		IMMP2L-related disorder	Benign (Jun 27, 2019)
7-110886673-A-G		not specified	Uncertain significance (Dec 16, 2023)
7-110886679-T-C		not specified	Uncertain significance (Oct 27, 2021)
7-110963057-T-G		IMMP2L-related disorder	Likely benign (Apr 30, 2019)
7-111122779-G-T		not specified	Uncertain significance (Sep 27, 2021)
7-111122785-C-A		not specified	Uncertain significance (Oct 03, 2022)
7-111122863-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-111122864-G-A			Benign (Feb 07, 2018)
7-111123037-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-111123100-A-G		not specified	Uncertain significance (Sep 07, 2022)
7-111123248-C-G		not specified	Uncertain significance (Feb 27, 2023)
7-111123447-A-G			Benign (Oct 09, 2017)
7-111123463-G-A		not specified	Uncertain significance (Nov 17, 2023)
7-111123553-A-C		not specified	Uncertain significance (Jun 22, 2023)
7-111123599-G-A		not specified	Uncertain significance (Feb 03, 2022)
7-111123634-G-C		not specified	Uncertain significance (Oct 12, 2022)
7-111123672-C-T			Benign (Oct 09, 2017)
7-111123833-T-C		not specified	Uncertain significance (Jan 30, 2024)
7-111123862-A-G		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IMMP2L	protein_coding	protein_coding	ENST00000405709	5	899464

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0112	0.851	125733	0	12	125745	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.173	96	101	0.951	0.00000558	1130
Missense in Polyphen		35	36.59	0.95655		407
Synonymous	-0.380	36	33.2	1.08	0.00000156	339
Loss of Function	1.21	4	7.60	0.526	3.20e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000440
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO. {ECO:0000269|PubMed:15814844}.
• Pathway: Protein export - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.284
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.196
• hipred: N
• hipred_score: 0.309
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.173

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Immp2l
• Phenotype: cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); reproductive system phenotype; pigmentation phenotype; neoplasm; endocrine/exocrine gland phenotype; vision/eye phenotype; immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: ovarian follicle development;signal peptide processing;protein processing involved in protein targeting to mitochondrion;superoxide metabolic process;cellular response to DNA damage stimulus;spermatogenesis;brain development;blood circulation;respiratory electron transport chain;ovulation;mitochondrial respiratory chain complex assembly;cerebellum vasculature development
• Cellular component: integral component of membrane;mitochondrial inner membrane peptidase complex
• Molecular function: peptidase activity;serine-type peptidase activity