NM_000454.5:c.25C>G

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PS1_ModeratePM1PM2PM5PP3_Moderate

The NM_000454.5(SOD1):ā€‹c.25C>Gā€‹(p.Leu9Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,544 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely pathogenic in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L9Q) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 0.0000021 ( 0 hom. )

Consequence

SOD1
NM_000454.5 missense

Scores

8
4
7

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.234
Variant links:
Genes affected
SOD1 (HGNC:11179): (superoxide dismutase 1) The protein encoded by this gene binds copper and zinc ions and is one of two isozymes responsible for destroying free superoxide radicals in the body. The encoded isozyme is a soluble cytoplasmic protein, acting as a homodimer to convert naturally-occuring but harmful superoxide radicals to molecular oxygen and hydrogen peroxide. The other isozyme is a mitochondrial protein. In addition, this protein contains an antimicrobial peptide that displays antibacterial, antifungal, and anti-MRSA activity against E. coli, E. faecalis, S. aureus, S. aureus MRSA LPV+, S. agalactiae, and yeast C. krusei. Mutations in this gene have been implicated as causes of familial amyotrophic lateral sclerosis. Rare transcript variants have been reported for this gene. [provided by RefSeq, Jul 2020]
SOD1-DT (HGNC:55683): (SOD1 divergent transcript)

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 10 ACMG points.

PS1
Transcript NM_000454.5 (SOD1) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in UniProt
PM1
In a strand (size 7) in uniprot entity SODC_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_000454.5
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.919

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SOD1NM_000454.5 linkc.25C>G p.Leu9Val missense_variant Exon 1 of 5 ENST00000270142.11 NP_000445.1
SOD1-DTNR_187558.1 linkn.231G>C non_coding_transcript_exon_variant Exon 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SOD1ENST00000270142.11 linkc.25C>G p.Leu9Val missense_variant Exon 1 of 5 1 NM_000454.5 ENSP00000270142.7 P00441
SOD1ENST00000389995.4 linkc.15+10C>G intron_variant Intron 1 of 4 3 ENSP00000374645.4 H7BYH4
SOD1ENST00000470944.1 linkn.86C>G non_coding_transcript_exon_variant Exon 1 of 5 2
SOD1ENST00000476106.5 linkn.102C>G non_coding_transcript_exon_variant Exon 1 of 5 5

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000205
AC:
3
AN:
1461544
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
727098
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Amyotrophic lateral sclerosis type 1 Uncertain:1
Aug 18, 2021
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SOD1 protein function. This variant is also known as Leu8Val. This missense change has been observed in individual(s) with amyotrophic lateral sclerosis (PMID: 14506936, 24908169, 28430856). This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with valine at codon 9 of the SOD1 protein (p.Leu9Val). The leucine residue is moderately conserved and there is a small physicochemical difference between leucine and valine. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.31
BayesDel_addAF
Pathogenic
0.35
D
BayesDel_noAF
Pathogenic
0.26
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Uncertain
0.57
D
Eigen
Benign
-0.22
Eigen_PC
Benign
-0.35
FATHMM_MKL
Benign
0.52
D
LIST_S2
Pathogenic
0.98
D
M_CAP
Pathogenic
0.97
D
MetaRNN
Pathogenic
0.92
D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Pathogenic
3.0
M
PrimateAI
Uncertain
0.69
T
PROVEAN
Benign
-2.3
N
REVEL
Pathogenic
0.70
Sift
Uncertain
0.020
D
Sift4G
Benign
0.077
T
Polyphen
0.91
P
Vest4
0.28
MutPred
0.88
Gain of methylation at K10 (P = 0.0436);
MVP
0.92
MPC
2.1
ClinPred
0.98
D
GERP RS
-0.48
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.47
gMVP
0.88

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1568807333; hg19: chr21-33032107; API