chr16-84482596-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_020947.4(MEAK7):c.1073G>T(p.Gly358Val) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,826 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G358R) has been classified as Uncertain significance.
Frequency
Consequence
NM_020947.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEAK7 | NM_020947.4 | c.1073G>T | p.Gly358Val | missense_variant | 6/8 | ENST00000343629.11 | |
MEAK7 | XM_005256075.3 | c.1073G>T | p.Gly358Val | missense_variant | 7/9 | ||
MEAK7 | XM_017023511.2 | c.1073G>T | p.Gly358Val | missense_variant | 6/8 | ||
MEAK7 | XM_047434410.1 | c.1073G>T | p.Gly358Val | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEAK7 | ENST00000343629.11 | c.1073G>T | p.Gly358Val | missense_variant | 6/8 | 1 | NM_020947.4 | P1 | |
MEAK7 | ENST00000566995.5 | c.*487G>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 | 5 | ||||
MEAK7 | ENST00000570036.5 | c.*1128G>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/9 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251364Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135838
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461826Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727214
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.1073G>T (p.G358V) alteration is located in exon 6 (coding exon 5) of the TLDC1 gene. This alteration results from a G to T substitution at nucleotide position 1073, causing the glycine (G) at amino acid position 358 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