chr11-71455169-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate
The NM_018161.5(NADSYN1):c.145T>C(p.Cys49Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000684 in 1,461,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_018161.5 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
NADSYN1 | NM_018161.5 | c.145T>C | p.Cys49Arg | missense_variant, splice_region_variant | 2/21 | ENST00000319023.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NADSYN1 | ENST00000319023.7 | c.145T>C | p.Cys49Arg | missense_variant, splice_region_variant | 2/21 | 1 | NM_018161.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251032Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135660
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461220Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726950
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Vertebral, cardiac, renal, and limb defects syndrome 3 Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Embryology Laboratory, Victor Chang Cardiac Research Institute | May 10, 2023 | - - |
Congenital NAD deficiency disorder Pathogenic:1
Pathogenic, no assertion criteria provided | research | Embryology Laboratory, Victor Chang Cardiac Research Institute | Dec 01, 2019 | This variant, c.145T>C, was found in compound heterozygosity with the pathogenic variant c.395G>T - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at