rs550138374
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_205836.3(FBXO38):c.3439A>G(p.Met1147Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,614,068 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
FBXO38
NM_205836.3 missense
NM_205836.3 missense
Scores
3
5
9
Clinical Significance
Conservation
PhyloP100: 7.07
Genes affected
FBXO38 (HGNC:28844): (F-box protein 38) This gene encodes a large protein that contains an F-box domain and may participate in protein ubiquitination. The encoded protein is a transcriptional co-activator of Krueppel-like factor 7 (Klf7). A heterozygous mutation in this gene was found in individuals with autosomal dominant distal hereditary motor neuronopathy type IID. There is a pseudogene for this gene on chromosome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, FBXO38
BP4
?
Computational evidence support a benign effect (MetaRNN=0.13936138).
BS2
?
High AC in GnomAdExome at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXO38 | NM_205836.3 | c.3439A>G | p.Met1147Val | missense_variant | 22/22 | ENST00000340253.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXO38 | ENST00000340253.10 | c.3439A>G | p.Met1147Val | missense_variant | 22/22 | 5 | NM_205836.3 | P3 | |
FBXO38 | ENST00000394370.7 | c.3214A>G | p.Met1072Val | missense_variant | 22/22 | 1 | A1 | ||
FBXO38 | ENST00000513826.1 | c.2704A>G | p.Met902Val | missense_variant | 20/20 | 1 | A1 | ||
FBXO38 | ENST00000296701.10 | c.2704A>G | p.Met902Val | missense_variant | 21/21 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152266Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251084Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135688
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GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461802Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727216
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74398
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Distal hereditary motor neuropathy type 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 14, 2023 | 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. This variant has not been reported in the literature in individuals affected with FBXO38-related conditions. This missense change has been observed in at least one individual who was not affected with FBXO38-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 576603). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). This variant is present in population databases (rs550138374, gnomAD 0.03%). This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1072 of the FBXO38 protein (p.Met1072Val). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;.
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;N;N
PrimateAI
Pathogenic
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Benign
Sift
Benign
T;D;D;T
Sift4G
Benign
T;T;T;T
Polyphen
B;D;P;B
Vest4
MutPred
0.25
.;Gain of sheet (P = 0.0061);.;.;
MVP
MPC
1.6
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