14-23556822-T-C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong

The NM_024328.6(THTPA):​c.65T>C​(p.Leu22Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

THTPA
NM_024328.6 missense

Scores

11
6
2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.74
Variant links:
Genes affected
THTPA (HGNC:18987): (thiamine triphosphatase) This gene encodes an enzyme which catalyzes the biosynthesis of thiamine disphophate (vitamin B1) by hydrolysis of thiamine triphosphate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2011]
ZFHX2-AS1 (HGNC:52658): (ZFHX2 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.97

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
THTPANM_024328.6 linkuse as main transcriptc.65T>C p.Leu22Pro missense_variant 1/2 ENST00000288014.7 NP_077304.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
THTPAENST00000288014.7 linkuse as main transcriptc.65T>C p.Leu22Pro missense_variant 1/21 NM_024328.6 ENSP00000288014 P1Q9BU02-1
ZFHX2-AS1ENST00000553985.1 linkuse as main transcriptn.239-1873T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsFeb 06, 2023The c.65T>C (p.L22P) alteration is located in exon 1 (coding exon 1) of the THTPA gene. This alteration results from a T to C substitution at nucleotide position 65, causing the leucine (L) at amino acid position 22 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.90
BayesDel_addAF
Pathogenic
0.38
D
BayesDel_noAF
Pathogenic
0.31
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.56
D;D;D;.;.;.
Eigen
Pathogenic
0.80
Eigen_PC
Pathogenic
0.74
FATHMM_MKL
Uncertain
0.82
D
LIST_S2
Benign
0.73
.;T;T;.;T;T
M_CAP
Pathogenic
0.33
D
MetaRNN
Pathogenic
0.97
D;D;D;D;D;D
MetaSVM
Uncertain
0.25
D
MutationAssessor
Pathogenic
3.7
H;H;.;H;.;H
MutationTaster
Benign
1.0
D;D;D;D;D
PrimateAI
Uncertain
0.63
T
PROVEAN
Pathogenic
-6.1
D;D;D;D;D;D
REVEL
Pathogenic
0.72
Sift
Pathogenic
0.0
D;D;D;D;D;D
Sift4G
Uncertain
0.0020
D;D;D;D;D;D
Polyphen
1.0
D;D;.;.;.;.
Vest4
0.85
MutPred
0.87
Loss of stability (P = 0.0215);Loss of stability (P = 0.0215);Loss of stability (P = 0.0215);Loss of stability (P = 0.0215);Loss of stability (P = 0.0215);Loss of stability (P = 0.0215);
MVP
0.97
MPC
0.13
ClinPred
1.0
D
GERP RS
5.8
Varity_R
0.98
gMVP
0.95

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-24026031; API