5-148982157-A-ATT
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_024577.4(SH3TC2):c.*22552_*22553dupAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00043 ( 0 hom., cov: 0)
Consequence
SH3TC2
NM_024577.4 3_prime_UTR
NM_024577.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
Genes affected
SH3TC2 (HGNC:29427): (SH3 domain and tetratricopeptide repeats 2) This gene encodes a protein with two N-terminal Src homology 3 (SH3) domains and 10 tetratricopeptide repeat (TPR) motifs, and is a member of a small gene family. The gene product has been proposed to be an adapter or docking molecule. Mutations in this gene result in autosomal recessive Charcot-Marie-Tooth disease type 4C, a childhood-onset neurodegenerative disease characterized by demyelination of motor and sensory neurons. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH3TC2 | NM_024577.4 | c.*22552_*22553dupAA | 3_prime_UTR_variant | 17/17 | ENST00000515425.6 | NP_078853.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH3TC2 | ENST00000515425 | c.*22552_*22553dupAA | 3_prime_UTR_variant | 17/17 | 1 | NM_024577.4 | ENSP00000423660.1 | |||
SH3TC2 | ENST00000504690.5 | n.*12+21567_*12+21568dupAA | intron_variant | 5 | ENSP00000425627.1 | |||||
SH3TC2 | ENST00000510350.1 | n.231+24722_231+24723dupAA | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000432 AC: 65AN: 150336Hom.: 0 Cov.: 0
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.000432 AC: 65AN: 150336Hom.: 0 Cov.: 0 AF XY: 0.000478 AC XY: 35AN XY: 73296
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Mononeuropathy of the Median Nerve Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Charcot-Marie-Tooth disease type 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at