chr2-69400386-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_001002755.4(NFU1):c.698C>T(p.Pro233Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,826 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. P233T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001002755.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFU1 | NM_001002755.4 | c.698C>T | p.Pro233Leu | missense_variant | 7/8 | ENST00000410022.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFU1 | ENST00000410022.7 | c.698C>T | p.Pro233Leu | missense_variant | 7/8 | 1 | NM_001002755.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152042Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251416Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135878
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461784Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727204
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.0000943 AC XY: 7AN XY: 74256
ClinVar
Submissions by phenotype
Multiple mitochondrial dysfunctions syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 27, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at