dbSNP rs1557331762: TMLHE:p.Glu392Gln (chrX-155491627-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_018196.4(TMLHE):c.1174G>C(p.Glu392Gln) variant causes a missense change. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 10)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

TMLHE
NM_018196.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.76

Publications

0 publications found

Variant links:

Genes affected

TMLHE (HGNC:18308): (trimethyllysine hydroxylase, epsilon) This gene encodes the protein trimethyllysine dioxygenase which is the first enzyme in the carnitine biosynthesis pathway. Carnitine play an essential role in the transport of activated fatty acids across the inner mitochondrial membrane. The encoded protein converts trimethyllysine into hydroxytrimethyllysine. A pseudogene of this gene is found on chromosome X. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

TMLHE links:

TMLHE-AS1 (HGNC:44261): (TMLHE antisense RNA 1)

TMLHE-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018196.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMLHE	NM_018196.4	MANE Select	c.1174G>C	p.Glu392Gln	missense	Exon 8 of 8	NP_060666.1	Q9NVH6-1
	TMLHE-AS1	NR_039991.1		n.472-1253C>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TMLHE	ENST00000334398.8	TSL:1 MANE Select	c.1174G>C	p.Glu392Gln	missense	Exon 8 of 8	ENSP00000335261.3	Q9NVH6-1
TMLHE-AS1	ENST00000433624.1	TSL:1	n.472-1253C>G		intron	N/A
TMLHE	ENST00000902557.1		c.1243G>C	p.Glu415Gln	missense	Exon 9 of 9	ENSP00000572616.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000122

AC:

AN:

82188

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000290

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

447195

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

124707

African (AFR)

AF:

0.00

AC:

AN:

13849

American (AMR)

AF:

0.00

AC:

AN:

14490

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11723

East Asian (EAS)

AF:

0.00

AC:

AN:

21783

South Asian (SAS)

AF:

0.00

AC:

AN:

33024

European-Finnish (FIN)

AF:

0.00

AC:

AN:

23512

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2157

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

303136

Other (OTH)

AF:

0.00

AC:

AN:

23521

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.37

BayesDel_addAF

Uncertain

0.064

BayesDel_noAF

Benign

-0.15

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.15

FATHMM_MKL

Uncertain

0.90

LIST_S2

Uncertain

0.91

M_CAP

Uncertain

0.11

MetaRNN

Uncertain

0.72

MetaSVM

Uncertain

-0.17

MutationAssessor

Benign

1.9

PhyloP100

6.8

PrimateAI

Pathogenic

0.85

PROVEAN

Benign

-0.58

REVEL

Uncertain

0.54

Sift

Benign

0.070

Sift4G

Benign

0.31

Polyphen

1.0

Vest4

0.59

MutPred

0.56

Gain of MoRF binding (P = 0.0413)

MVP

0.42

MPC

0.76

ClinPred

0.56

GERP RS

2.7

Varity_R

0.22

gMVP

0.36

Mutation Taster

=53/47

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over