2-85544938-ATTTTT-ATTTT
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_000821.7(GGCX):c.*4995delA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000462 in 147,068 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.033 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GGCX
NM_000821.7 3_prime_UTR
NM_000821.7 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.263
Publications
0 publications found
Genes affected
GGCX (HGNC:4247): (gamma-glutamyl carboxylase) This gene encodes an integral membrane protein of the rough endoplasmic reticulum that carboxylates glutamate residues of vitamin K-dependent proteins to gamma carboxyl glutamate, a modification that is required for their activity. The vitamin K-dependent protein substrates have a propeptide that binds the enzyme, with carbon dioxide, dioxide, and reduced vitamin K acting as co-substrates. Vitamin K-dependent proteins affect a number of physiologic processes including blood coagulation, prevention of vascular calcification, and inflammation. Allelic variants of this gene have been associated with pseudoxanthoma elasticum-like disorder with associated multiple coagulation factor deficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
MAT2A (HGNC:6904): (methionine adenosyltransferase 2A) The protein encoded by this gene catalyzes the production of S-adenosylmethionine (AdoMet) from methionine and ATP. AdoMet is the key methyl donor in cellular processes. [provided by RefSeq, Jun 2011]
MAT2A Gene-Disease associations (from GenCC):
- familial thoracic aortic aneurysm and aortic dissectionInheritance: AD Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GGCX | NM_000821.7 | c.*4995delA | 3_prime_UTR_variant | Exon 15 of 15 | ENST00000233838.9 | NP_000812.2 | ||
| MAT2A | NM_005911.6 | c.*1178delT | 3_prime_UTR_variant | Exon 9 of 9 | ENST00000306434.8 | NP_005902.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| GGCX | ENST00000233838.9 | c.*4995delA | 3_prime_UTR_variant | Exon 15 of 15 | 1 | NM_000821.7 | ENSP00000233838.3 | |||
| MAT2A | ENST00000306434.8 | c.*1178delT | 3_prime_UTR_variant | Exon 9 of 9 | 1 | NM_005911.6 | ENSP00000303147.3 |
Frequencies
GnomAD3 genomes 0.000463 AC: 68AN: 147002Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
68
AN:
147002
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 Data not reliable, filtered out with message: AS_VQSR AF: 0.0327 AC: 11AN: 336Hom.: 0 Cov.: 0 AF XY: 0.0409 AC XY: 9AN XY: 220 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
11
AN:
336
Hom.:
Cov.:
0
AF XY:
AC XY:
9
AN XY:
220
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)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
9
AN:
326
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
2
AN:
6
Other (OTH)
AF:
AC:
0
AN:
4
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.248
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.000462 AC: 68AN: 147068Hom.: 0 Cov.: 32 AF XY: 0.000559 AC XY: 40AN XY: 71560 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
68
AN:
147068
Hom.:
Cov.:
32
AF XY:
AC XY:
40
AN XY:
71560
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
23
AN:
40378
American (AMR)
AF:
AC:
5
AN:
14716
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3392
East Asian (EAS)
AF:
AC:
2
AN:
5010
South Asian (SAS)
AF:
AC:
3
AN:
4636
European-Finnish (FIN)
AF:
AC:
15
AN:
9454
Middle Eastern (MID)
AF:
AC:
0
AN:
278
European-Non Finnish (NFE)
AF:
AC:
19
AN:
66286
Other (OTH)
AF:
AC:
1
AN:
2016
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.382
Heterozygous variant carriers
0
6
12
17
23
29
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
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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