X-43949887-G-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_ModeratePP5_Moderate
The NM_000266.4(NDP):c.314C>T(p.Ala105Val) variant causes a missense change involving the alteration of a conserved nucleotide. 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A105T) has been classified as Pathogenic.
Frequency
Consequence
NM_000266.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDP | NM_000266.4 | c.314C>T | p.Ala105Val | missense_variant | 3/3 | ENST00000642620.1 | |
NDP-AS1 | NR_046631.1 | n.156G>A | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDP | ENST00000642620.1 | c.314C>T | p.Ala105Val | missense_variant | 3/3 | NM_000266.4 | P1 | ||
NDP-AS1 | ENST00000435093.1 | n.156G>A | non_coding_transcript_exon_variant | 1/5 | 3 | ||||
NDP | ENST00000647044.1 | c.314C>T | p.Ala105Val | missense_variant | 4/4 | P1 | |||
NDP | ENST00000470584.1 | n.358C>T | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Nystagmus;C0266568:Persistent hyperplastic primary vitreous;C0271183:High myopia;C0426501:Short lingual frenulum Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Dec 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at