chr5-126542500-CA-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001182.5(ALDH7A1):c.*2464delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.10 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ALDH7A1
NM_001182.5 3_prime_UTR
NM_001182.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.291
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: Orphanet, ClinGen, Illumina
- 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: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001182.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ALDH7A1 | NM_001182.5 | MANE Select | c.*2464delT | 3_prime_UTR | Exon 18 of 18 | NP_001173.2 | P49419-1 | ||
| ALDH7A1 | NM_001201377.2 | c.*2464delT | 3_prime_UTR | Exon 18 of 18 | NP_001188306.1 | P49419-2 | |||
| ALDH7A1 | NM_001202404.2 | c.*2464delT | 3_prime_UTR | Exon 16 of 16 | NP_001189333.2 | P49419-4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ALDH7A1 | ENST00000409134.8 | TSL:1 MANE Select | c.*2464delT | 3_prime_UTR | Exon 18 of 18 | ENSP00000387123.3 | P49419-1 | ||
| ALDH7A1 | ENST00000635851.1 | TSL:5 | c.1563-1513delT | intron | N/A | ENSP00000490819.1 | A0A1B0GW82 | ||
| ALDH7A1 | ENST00000637782.1 | TSL:5 | c.1565+3823delT | intron | N/A | ENSP00000490024.1 | A0A1B0GUA1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 150512Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
150512
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.100 AC: 2AN: 20Hom.: 0 Cov.: 0 AF XY: 0.111 AC XY: 2AN XY: 18 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
2
AN:
20
Hom.:
Cov.:
0
AF XY:
AC XY:
2
AN XY:
18
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
4
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
1
AN:
16
Other (OTH)
AC:
0
AN:
0
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00 AC: 0AN: 150512Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73346
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
150512
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
73346
African (AFR)
AF:
AC:
0
AN:
40928
American (AMR)
AF:
AC:
0
AN:
15060
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3462
East Asian (EAS)
AF:
AC:
0
AN:
5154
South Asian (SAS)
AF:
AC:
0
AN:
4744
European-Finnish (FIN)
AF:
AC:
0
AN:
10230
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67644
Other (OTH)
AF:
AC:
0
AN:
2068
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
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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