MTIF3

mitochondrial translational initiation factor 3

Basic information

Region (hg38): 13:27435643-27450591

Links

ENSG00000122033 ∙ NCBI:219402 ∙ OMIM:619554 ∙ HGNC:29788 ∙ Uniprot:Q9H2K0 ∙ 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 MTIF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTIF3 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 MTIF3

This is a list of pathogenic ClinVar variants found in the MTIF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-27435721-T-G		not specified	Uncertain significance (Jul 20, 2021)
13-27435826-G-A		not specified	Uncertain significance (Oct 04, 2022)
13-27435845-A-G		not specified	Uncertain significance (May 31, 2023)
13-27437222-T-A		not specified	Uncertain significance (May 23, 2023)
13-27437228-T-G		not specified	Uncertain significance (Feb 28, 2023)
13-27440010-C-G		not specified	Uncertain significance (Dec 15, 2022)
13-27440031-G-A		not specified	Uncertain significance (Aug 30, 2021)
13-27440036-T-C			Likely benign (Aug 15, 2017)
13-27440114-C-T		not specified	Uncertain significance (Oct 02, 2023)
13-27440162-T-C		not specified	Uncertain significance (Jan 11, 2023)
13-27440217-C-T		not specified	Likely benign (May 30, 2023)
13-27440288-G-C		not specified	Uncertain significance (Mar 25, 2024)
13-27440435-A-G		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTIF3	protein_coding	protein_coding	ENST00000381116	3	14964

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.90e-7	0.211	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.351	130	142	0.917	0.00000715	1836
Missense in Polyphen		36	37.499	0.96002		500
Synonymous	0.00418	51	51.0	0.999	0.00000259	522
Loss of Function	0.100	10	10.3	0.966	8.03e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000363	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000202	0.000202
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: IF-3 binds to the 28S ribosomal subunit and shifts the equilibrum between 55S ribosomes and their 39S and 28S subunits in favor of the free subunits, thus enhancing the availability of 28S subunits on which protein synthesis initiation begins. {ECO:0000269|PubMed:12095986}.
• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.0398

Intolerance Scores

• loftool: 0.989
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.00894
• hipred: N
• hipred_score: 0.145
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.214

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtif3

Gene ontology

• Biological process: ribosome disassembly;mitochondrial translational initiation
• Cellular component: mitochondrion
• Molecular function: translation initiation factor activity;protein binding;translation factor activity, RNA binding;ribosome binding;ribosomal small subunit binding