rs978958073
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001182.5(ALDH7A1):c.1374C>T(p.Ser458Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,232 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 Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
ALDH7A1
NM_001182.5 synonymous
NM_001182.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.726
Publications
0 publications found
Genes affected
ALDH7A1 (HGNC:877): (aldehyde dehydrogenase 7 family member A1) The protein encoded by this gene is a member of subfamily 7 in the aldehyde dehydrogenase gene family. These enzymes are thought to play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. This particular member has homology to a previously described protein from the green garden pea, the 26g pea turgor protein. It is also involved in lysine catabolism that is known to occur in the mitochondrial matrix. Recent reports show that this protein is found both in the cytosol and the mitochondria, and the two forms likely arise from the use of alternative translation initiation sites. An additional variant encoding a different isoform has also been found for this gene. Mutations in this gene are associated with pyridoxine-dependent epilepsy. Several related pseudogenes have also been identified. [provided by RefSeq, Jan 2011]
ALDH7A1 Gene-Disease associations (from GenCC):
- pyridoxine-dependent epilepsyInheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: Illumina, Orphanet, ClinGen
- pyridoxine-dependent epilepsy caused by ALDH7A1 mutantInheritance: AR, AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 5-126550237-G-A is Benign according to our data. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-126550237-G-A is described in CliVar as Likely_benign. Clinvar id is 416194.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.726 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ALDH7A1 | NM_001182.5 | c.1374C>T | p.Ser458Ser | synonymous_variant | Exon 15 of 18 | ENST00000409134.8 | NP_001173.2 | |
| ALDH7A1 | NM_001201377.2 | c.1290C>T | p.Ser430Ser | synonymous_variant | Exon 15 of 18 | NP_001188306.1 | ||
| ALDH7A1 | NM_001202404.2 | c.1182C>T | p.Ser394Ser | synonymous_variant | Exon 13 of 16 | NP_001189333.2 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.0000159 AC: 4AN: 251254 AF XY: 0.00000736 show subpopulations
GnomAD2 exomes
AF:
AC:
4
AN:
251254
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461232Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726934 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1461232
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
726934
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33462
American (AMR)
AF:
AC:
2
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
0
AN:
39678
South Asian (SAS)
AF:
AC:
0
AN:
86226
European-Finnish (FIN)
AF:
AC:
0
AN:
53328
Middle Eastern (MID)
AF:
AC:
0
AN:
5394
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111944
Other (OTH)
AF:
AC:
2
AN:
60346
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Pyridoxine-dependent epilepsy Benign:1
Oct 24, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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