rs370111257
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 1P and 2B. PP2BP4BP6
The NM_000702.4(ATP1A2):c.1288G>A(p.Val430Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000702.4 missense
Scores
Clinical Significance
Conservation
Publications
- hemiplegic migraine-developmental and epileptic encephalopathy spectrumInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- migraine, familial hemiplegic, 2Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
- alternating hemiplegia of childhood 1Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
- developmental and epileptic encephalopathy 98Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
- fetal akinesia, respiratory insufficiency, microcephaly, polymicrogyria, and dysmorphic faciesInheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- alternating hemiplegia of childhoodInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial or sporadic hemiplegic migraineInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP1A2 | NM_000702.4 | c.1288G>A | p.Val430Ile | missense_variant | Exon 10 of 23 | ENST00000361216.8 | NP_000693.1 | |
ATP1A2 | XM_047421286.1 | c.397G>A | p.Val133Ile | missense_variant | Exon 3 of 16 | XP_047277242.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP1A2 | ENST00000361216.8 | c.1288G>A | p.Val430Ile | missense_variant | Exon 10 of 23 | 1 | NM_000702.4 | ENSP00000354490.3 | ||
ATP1A2 | ENST00000392233.7 | c.1288G>A | p.Val430Ile | missense_variant | Exon 10 of 23 | 5 | ENSP00000376066.3 | |||
ATP1A2 | ENST00000447527.1 | c.418G>A | p.Val140Ile | missense_variant | Exon 3 of 16 | 2 | ENSP00000411705.1 | |||
ATP1A2 | ENST00000472488.5 | n.1391G>A | non_coding_transcript_exon_variant | Exon 10 of 20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152192Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000241 AC: 6AN: 248882 AF XY: 0.0000297 show subpopulations
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460814Hom.: 0 Cov.: 34 AF XY: 0.0000151 AC XY: 11AN XY: 726570 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74482 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Uncertain:1
BS2 -
Familial hemiplegic migraine Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at