11-108158984-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002519.3(NPAT):c.4242G>A(p.Met1414Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002519.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPAT | NM_002519.3 | c.4242G>A | p.Met1414Ile | missense_variant | Exon 18 of 18 | ENST00000278612.9 | NP_002510.2 | |
NPAT | NM_001321307.1 | c.4263G>A | p.Met1421Ile | missense_variant | Exon 18 of 18 | NP_001308236.1 | ||
NPAT | XM_011542854.3 | c.4269G>A | p.Met1423Ile | missense_variant | Exon 18 of 18 | XP_011541156.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPAT | ENST00000278612.9 | c.4242G>A | p.Met1414Ile | missense_variant | Exon 18 of 18 | 1 | NM_002519.3 | ENSP00000278612.8 | ||
NPAT | ENST00000530859.1 | n.1615G>A | non_coding_transcript_exon_variant | Exon 5 of 5 | 2 | |||||
NPAT | ENST00000530926.1 | n.399G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 27
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
This sequence change does not appear to have been previously described in individuals with NPAT-related disorders and has also not been described in the population databases such as ExAC and gnomAD. The p.Met1414Ile change affects a highly conserved amino acid residue located in a domain of the NPAT protein that is not known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Met1414Ile substitution. Due to insufficient evidence and the lack of functional studies, the clinical significance of the p.Met1414Ile change remains unknown at this time. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.