MPV17L2

MPV17 mitochondrial inner membrane protein like 2

Basic information

Region (hg38): 19:18193217-18196948

Links

ENSG00000254858 ∙ NCBI:84769 ∙ OMIM:616133 ∙ HGNC:28177 ∙ Uniprot:Q567V2 ∙ 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 MPV17L2 gene.

• Inborn genetic diseases (6 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPV17L2 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			6		1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in MPV17L2

This is a list of pathogenic ClinVar variants found in the MPV17L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18193294-G-A		not specified	Uncertain significance (Dec 23, 2022)
19-18193313-G-A			not provided (-)
19-18193352-C-T		not specified	Uncertain significance (May 28, 2023)
19-18193394-C-A		not specified	Uncertain significance (Oct 31, 2022)
19-18193890-A-G			Benign (Jan 10, 2019)
19-18194813-G-A		not specified	Uncertain significance (Jul 20, 2022)
19-18195022-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-18196002-C-A		not specified	Uncertain significance (May 23, 2023)
19-18196042-C-T		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPV17L2	protein_coding	protein_coding	ENST00000599612	5	3767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.43e-7	0.274	124753	0	47	124800	0.000188

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.334	103	113	0.912	0.00000597	1271
Missense in Polyphen		26	40.84	0.63663		467
Synonymous	1.38	39	51.6	0.756	0.00000276	442
Loss of Function	0.276	10	11.0	0.910	5.70e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000442	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000115
Middle Eastern	0.000278	0.000278
South Asian	0.000733	0.000719
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the assembly and stability of the mitochondrial ribosome (PubMed:24948607). Is a positive regulator of mitochondrial protein synthesis (PubMed:24948607). {ECO:0000269|PubMed:24948607}.
• Pathway: Peroxisome - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.591
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.248
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.372

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpv17l2

Gene ontology

• Biological process: mitochondrial ribosome assembly;positive regulation of mitochondrial translation
• Cellular component: cytoplasm;mitochondrial inner membrane;mitochondrial large ribosomal subunit;integral component of membrane