10-133395773-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_138384.4(MTG1):c.173C>T(p.Ala58Val) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,618 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138384.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTG1 | ENST00000317502.11 | c.173C>T | p.Ala58Val | missense_variant | Exon 2 of 11 | 1 | NM_138384.4 | ENSP00000323047.6 | ||
MTG1 | ENST00000477902.6 | c.50C>T | p.Ala17Val | missense_variant | Exon 2 of 11 | 3 | ENSP00000475596.1 | |||
ENSG00000254536 | ENST00000468317.3 | n.*97C>T | non_coding_transcript_exon_variant | Exon 7 of 16 | 5 | ENSP00000436767.2 | ||||
ENSG00000254536 | ENST00000670407.1 | n.*339C>T | non_coding_transcript_exon_variant | Exon 6 of 7 | ENSP00000499264.1 | |||||
ENSG00000254536 | ENST00000468317.3 | n.*97C>T | 3_prime_UTR_variant | Exon 7 of 16 | 5 | ENSP00000436767.2 | ||||
ENSG00000254536 | ENST00000670407.1 | n.*339C>T | 3_prime_UTR_variant | Exon 6 of 7 | ENSP00000499264.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461618Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727082
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.173C>T (p.A58V) alteration is located in exon 2 (coding exon 2) of the MTG1 gene. This alteration results from a C to T substitution at nucleotide position 173, causing the alanine (A) at amino acid position 58 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at