TMLHE
Basic information
Region (hg38): X:155489011-155719098
Links
Phenotypes
GenCC
Source:
- epsilon-trimethyllysine hydroxylase deficiency (Limited), mode of inheritance: Unknown
- autism spectrum disorder (Disputed Evidence), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Epsilon-trimethyllysine hydroxylase deficiency | AD | Biochemical | The condition may be associated with autism, and carnitine supplementation has been reported as beneficial related to developmental milestones | Biochemical; Neurologic | 21865298; 22566635; 25943046 |
ClinVar
This is a list of variants' phenotypes submitted to
- Epsilon-trimethyllysine hydroxylase deficiency (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMLHE 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 | 8 | |||||
| missense | 23 | 27 | ||||
| nonsense | 5 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 1 | 0 | 29 | 10 | 1 |
Variants in TMLHE
This is a list of pathogenic ClinVar variants found in the TMLHE region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TMLHE | protein_coding | protein_coding | ENST00000334398 | 7 | 179830 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000796 | 0.777 | 125709 | 12 | 16 | 125737 | 0.000111 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.637 | 112 | 133 | 0.844 | 0.00000987 | 2753 |
| Missense in Polyphen | 37 | 47.984 | 0.77109 | 933 | ||
| Synonymous | -0.348 | 54 | 50.8 | 1.06 | 0.00000380 | 786 |
| Loss of Function | 1.13 | 8 | 12.3 | 0.652 | 8.29e-7 | 250 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000431 | 0.000415 |
| Ashkenazi Jewish | 0.000134 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000627 | 0.0000462 |
| European (Non-Finnish) | 0.0000998 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000449 | 0.000261 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Converts trimethyllysine (TML) into hydroxytrimethyllysine (HTML) (PubMed:11431483, PubMed:23092983). {ECO:0000269|PubMed:11431483, ECO:0000269|PubMed:23092983}.;
- Pathway
- Lysine degradation - Homo sapiens (human);Carnitine Synthesis;Branched-chain amino acid catabolism;Metabolism of amino acids and derivatives;Metabolism;Lysine degradation;Lysine metabolism;Carnitine synthesis;L-carnitine biosynthesis
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.228
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.29
Haploinsufficiency Scores
- pHI
- 0.194
- hipred
- N
- hipred_score
- 0.350
- ghis
- 0.455
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.879
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tmlhe
- Phenotype
Gene ontology
- Biological process
- carnitine biosynthetic process;oxidation-reduction process
- Cellular component
- mitochondrion;mitochondrial matrix
- Molecular function
- iron ion binding;protein binding;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;trimethyllysine dioxygenase activity