rs1553313839
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM4PP3
The NM_018713.3(SLC30A10):c.292_402del(p.Val98_Phe134del) variant causes a conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000698 in 1,433,684 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
SLC30A10
NM_018713.3 conservative_inframe_deletion
NM_018713.3 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.79
Publications
2 publications found
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]
SLC30A10 Gene-Disease associations (from GenCC):
- cirrhosis - dystonia - polycythemia - hypermanganesemia syndromeInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Genomics England PanelApp
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_018713.3.
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLC30A10 | NM_018713.3 | c.292_402del | p.Val98_Phe134del | conservative_inframe_deletion | Exon 1 of 4 | ENST00000366926.4 | NP_061183.2 | |
| SLC30A10 | NM_001416005.1 | c.-422_-312del | 5_prime_UTR_variant | Exon 1 of 4 | NP_001402934.1 | |||
| SLC30A10 | NM_001376929.1 | c.452-1044_452-934del | intron_variant | Intron 1 of 3 | NP_001363858.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLC30A10 | ENST00000366926.4 | c.292_402del | p.Val98_Phe134del | conservative_inframe_deletion | Exon 1 of 4 | 1 | NM_018713.3 | ENSP00000355893.4 | ||
| SLC30A10 | ENST00000356609.2 | n.292_402del | non_coding_transcript_exon_variant | Exon 1 of 4 | 1 | ENSP00000349018.2 | ||||
| SLC30A10 | ENST00000696608.1 | c.452-1044_452-934del | intron_variant | Intron 1 of 3 | ENSP00000512752.1 | |||||
| SLC30A10 | ENST00000484239.5 | n.81-1044_81-934del | intron_variant | Intron 1 of 8 | 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.98e-7 AC: 1AN: 1433684Hom.: 0 AF XY: 0.00000141 AC XY: 1AN XY: 710832 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1433684
Hom.:
AF XY:
AC XY:
1
AN XY:
710832
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
32360
American (AMR)
AF:
AC:
0
AN:
41768
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25630
East Asian (EAS)
AF:
AC:
0
AN:
37300
South Asian (SAS)
AF:
AC:
0
AN:
81972
European-Finnish (FIN)
AF:
AC:
0
AN:
49780
Middle Eastern (MID)
AF:
AC:
0
AN:
5742
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1099848
Other (OTH)
AF:
AC:
0
AN:
59284
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
Hypermanganesemia with dystonia, polycythemia, and cirrhosis Other:1
-
GeneReviews
Significance:not provided
Review Status:no classification provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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