TEFM

transcription elongation factor, mitochondrial

Basic information

Region (hg38): 17:30897336-30906238

Previous symbols: [ "C17orf42" ]

Links

ENSG00000172171 ∙ NCBI:79736 ∙ OMIM:616422 ∙ HGNC:26223 ∙ Uniprot:Q96QE5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 58	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Musculoskeletal; Neurologic; Ophthalmologic	32313153; 36823193

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TEFM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEFM 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in TEFM

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

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

Position	Type	Phenotype	Significance	ClinVar
17-30899248-T-C		not specified	Uncertain significance (Sep 14, 2022)
17-30899286-T-C		not specified	Uncertain significance (Jul 06, 2022)
17-30899303-A-G		not specified	Uncertain significance (Nov 29, 2021)
17-30899436-C-A		not specified	Uncertain significance (Aug 02, 2023)
17-30899484-C-T		not specified	Uncertain significance (Jun 23, 2023)
17-30899543-A-G		not specified	Uncertain significance (Sep 17, 2021)
17-30899566-T-C		not specified	Uncertain significance (Oct 03, 2023)
17-30900440-T-C		not specified	Uncertain significance (Jan 23, 2023)
17-30900495-T-C		not specified	Uncertain significance (May 26, 2022)
17-30900510-G-A		not specified	Uncertain significance (Dec 22, 2023)
17-30900543-G-T		not specified	Uncertain significance (May 09, 2023)
17-30904116-G-A		not specified	Uncertain significance (May 10, 2024)
17-30904148-G-C		not specified	Uncertain significance (Mar 20, 2024)
17-30904187-C-T		not specified	Uncertain significance (Apr 19, 2023)
17-30904221-T-C		not specified	Uncertain significance (Aug 21, 2023)
17-30904255-G-C		not specified	Uncertain significance (Jan 26, 2023)
17-30904478-A-G		not specified	Uncertain significance (Jun 02, 2023)
17-30904487-T-C		not specified	Uncertain significance (Apr 24, 2024)
17-30904515-A-C		not specified	Uncertain significance (Oct 05, 2022)
17-30904526-C-T		not specified	Uncertain significance (Dec 20, 2023)
17-30906193-G-C		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEFM	protein_coding	protein_coding	ENST00000581216	4	9485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.514	0.485	124771	0	22	124793	0.0000882

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.584	173	196	0.883	0.0000106	2347
Missense in Polyphen		43	57.64	0.74601		737
Synonymous	1.86	54	74.4	0.726	0.00000392	697
Loss of Function	2.86	3	14.9	0.201	8.44e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000874	0.0000874
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000334	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.0000895	0.0000883
Middle Eastern	0.000334	0.000334
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription elongation factor which increases mitochondrial RNA polymerase processivity. Regulates transcription of the mitochondrial genome, including genes important for the oxidative phosphorylation machinery. {ECO:0000269|PubMed:21278163}.

Recessive Scores

• pRec: 0.0741

Intolerance Scores

• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.0944
• hipred: N
• hipred_score: 0.145
• ghis: 0.599

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tefm

Gene ontology

• Biological process: oxidative phosphorylation;mitochondrial DNA replication;mitochondrial transcription;transcription elongation from mitochondrial promoter
• Cellular component: mitochondrion;mitochondrial matrix;mitochondrial nucleoid;ribonucleoprotein complex
• Molecular function: RNA binding;protein binding;crossover junction endodeoxyribonuclease activity;DNA polymerase processivity factor activity