rs281860288
Variant names:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_018713.3(SLC30A10):c.585delG(p.Thr196ProfsTer17) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC30A10
NM_018713.3 frameshift
NM_018713.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0440
Genes affected
SLC30A10 (HGNC:25355): (solute carrier family 30 member 10) This gene is highly expressed in the liver and is inducible by manganese. Its protein product appears to be critical in maintaining manganese levels, and has higher specificity for manganese than zinc. Loss of function mutations appear to result in a pleomorphic phenotype, including dystonia and adult-onset parkinsonism. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-219927855-TC-T is Pathogenic according to our data. Variant chr1-219927855-TC-T is described in ClinVar as [Pathogenic]. Clinvar id is 30887.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-219927855-TC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC30A10 | NM_018713.3 | c.585delG | p.Thr196ProfsTer17 | frameshift_variant | Exon 1 of 4 | ENST00000366926.4 | NP_061183.2 | |
SLC30A10 | NM_001416005.1 | c.-129delG | 5_prime_UTR_variant | Exon 1 of 4 | NP_001402934.1 | |||
SLC30A10 | NM_001376929.1 | c.452-751delG | intron_variant | Intron 1 of 3 | NP_001363858.1 | |||
SLC30A10 | NM_001416004.1 | c.-786delG | upstream_gene_variant | NP_001402933.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC30A10 | ENST00000366926.4 | c.585delG | p.Thr196ProfsTer17 | frameshift_variant | Exon 1 of 4 | 1 | NM_018713.3 | ENSP00000355893.4 | ||
SLC30A10 | ENST00000356609.2 | n.585delG | non_coding_transcript_exon_variant | Exon 1 of 4 | 1 | ENSP00000349018.2 | ||||
SLC30A10 | ENST00000696608.1 | c.452-751delG | intron_variant | Intron 1 of 3 | ENSP00000512752.1 | |||||
SLC30A10 | ENST00000484239.5 | n.81-751delG | intron_variant | Intron 1 of 8 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1393488Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 688056
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1393488
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
688056
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hypermanganesemia with dystonia, polycythemia, and cirrhosis Pathogenic:1Other:1
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GeneReviews
Significance: not provided
Review Status: no classification provided
Collection Method: literature only
- -
Mar 09, 2012
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only
- -
not provided Pathogenic:1
Aug 09, 2016
Eurofins Ntd Llc (ga)
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
Calibrated prediction
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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