1-59321662-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018291.5(FGGY):āc.113A>Gā(p.Asp38Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000089 in 1,461,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000089 ( 0 hom. )
Consequence
FGGY
NM_018291.5 missense
NM_018291.5 missense
Scores
1
2
16
Clinical Significance
Conservation
PhyloP100: 6.53
Genes affected
FGGY (HGNC:25610): (FGGY carbohydrate kinase domain containing) This gene encodes a protein that phosphorylates carbohydrates such as ribulose, ribitol, and L-arabinitol. Genome-wide association studies in some populations have found an association between polymorphisms in this gene and sporadic amyotrophic lateral sclerosis, but studies of other populations have not been able to replicate this association. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2170184).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FGGY | NM_018291.5 | c.113A>G | p.Asp38Gly | missense_variant | 2/16 | ENST00000303721.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGGY | ENST00000303721.12 | c.113A>G | p.Asp38Gly | missense_variant | 2/16 | 1 | NM_018291.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247234Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134416
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GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461016Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726728
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GnomAD4 genome Cov.: 32
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32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.113A>G (p.D38G) alteration is located in exon 2 (coding exon 1) of the FGGY gene. This alteration results from a A to G substitution at nucleotide position 113, causing the aspartic acid (D) at amino acid position 38 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;N;N;N
MutationTaster
Benign
D;D;N
PrimateAI
Benign
T
PROVEAN
Benign
.;N;N;N;N
REVEL
Benign
Sift
Benign
.;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
0.0
.;.;B;B;.
Vest4
0.34, 0.29, 0.32
MutPred
Loss of ubiquitination at K42 (P = 0.063);Loss of ubiquitination at K42 (P = 0.063);Loss of ubiquitination at K42 (P = 0.063);Loss of ubiquitination at K42 (P = 0.063);Loss of ubiquitination at K42 (P = 0.063);
MVP
MPC
0.029
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at