NM_001397406.1:c.447G>C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001397406.1(FDX2):c.447G>C(p.Leu149Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,870 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: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
FDX2
NM_001397406.1 synonymous
NM_001397406.1 synonymous
Scores
1
1
1
Clinical Significance
Conservation
PhyloP100: 1.26
Publications
0 publications found
Genes affected
FDX2 (HGNC:30546): (ferredoxin 2) This gene encodes a member of the ferredoxin family. The encoded protein contains a 2Fe-2S ferredoxin-type domain and is essential for heme A and Fe/S protein biosynthesis. Mutation in FDX1L gene is associated with mitochondrial muscle myopathy. [provided by RefSeq, Sep 2014]
FDX2 Gene-Disease associations (from GenCC):
- mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathyInheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
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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 (REVEL=0.018).
BP6
Variant 19-10310591-C-G is Benign according to our data. Variant chr19-10310591-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2987628.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.26 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001397406.1. 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 |
|---|---|---|---|---|---|---|---|---|---|
| FDX2 | NM_001397406.1 | MANE Select | c.447G>C | p.Leu149Leu | synonymous | Exon 5 of 5 | NP_001384335.1 | Q6P4F2-1 | |
| FDX2-ZGLP1 | NR_176051.1 | n.466G>C | non_coding_transcript_exon | Exon 5 of 8 | |||||
| FDX2-ZGLP1 | NR_176052.1 | n.527G>C | non_coding_transcript_exon | Exon 5 of 9 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FDX2 | ENST00000393708.3 | TSL:1 MANE Select | c.447G>C | p.Leu149Leu | synonymous | Exon 5 of 5 | ENSP00000377311.5 | Q6P4F2-1 | |
| ENSG00000167807 | ENST00000452032.6 | TSL:2 | n.410G>C | non_coding_transcript_exon | Exon 5 of 11 | ENSP00000408510.3 | E7EQL1 | ||
| FDX2 | ENST00000492239.5 | TSL:2 | c.42G>C | p.Leu14Leu | synonymous | Exon 4 of 4 | ENSP00000488228.1 | A0A0A0MTS8 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727238 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461870
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
727238
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53408
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1112006
Other (OTH)
AF:
AC:
0
AN:
60394
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_noAF
Pathogenic
DANN
Uncertain
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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