NM_001676.7:c.613A>T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001676.7(ATP12A):c.613A>T(p.Ile205Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,461,868 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. I205V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001676.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP12A | ENST00000381946.5 | c.613A>T | p.Ile205Phe | missense_variant | Exon 6 of 23 | 1 | NM_001676.7 | ENSP00000371372.3 | ||
ATP12A | ENST00000218548.10 | c.613A>T | p.Ile205Phe | missense_variant | Exon 6 of 23 | 1 | ENSP00000218548.6 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251482Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135916
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727244
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.613A>T (p.I205F) alteration is located in exon 6 (coding exon 6) of the ATP12A gene. This alteration results from a A to T substitution at nucleotide position 613, causing the isoleucine (I) at amino acid position 205 to be replaced by a phenylalanine (F). 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