Classification
Category 1
CMH MAF
12 /
14969 samples
(0.0802%)
12 het.,
0 hom.
(100%)
12 /
29938 total alleles
(0.0401%)
Genes
gene: CTNS
synonym(s): CTNS-LSB, PQLC4, CTNS, ENSG00000040531
NM_001031681.2
[CDS]
hgvs_c: NM_001031681.2:c.589G>A
reference AA: G
variant AA: R
reference codon: Gga
variant codon: Aga
cDNA pos: 1059
CDS pos: 589
translation impact: non_synonymous
protein sequence:
NP_001026851.2
AA pos: 197
hgvs_p: NP_001026851.2:p.Gly197Arg
blosum: -2
SIFT: deleterious (0.03)
PolyPhen2: probably_damaging (0.997)
NM_004937.2
[CDS]
Reportable
hgvs_c: NM_004937.2:c.589G>A
reference AA: G
variant AA: R
reference codon: Gga
variant codon: Aga
cDNA pos: 1182
CDS pos: 589
translation impact: non_synonymous
protein sequence:
NP_004928.2
AA pos: 197
hgvs_p: NP_004928.2:p.Gly197Arg
blosum: -2
SIFT: deleterious (0.03)
PolyPhen2: probably_damaging (0.994)
dbSNP
rs113994207
TOPMED_MAF = 0.00012742099898063
ClinVar
4451
clinvar_significance = Pathogenic_Likely_pathogenic
clinvar_disease = Nephropathic cystinosis
clinvar_disease = Juvenile nephropathic cystinosis
clinvar_disease = Cystinosis
ExAC
ExAC
| Ethnicity |
Count / Number |
MAF |
| African |
1 / 10350 |
0.00966% |
| America/Latino |
0 / 11562 |
0% |
| East Asian |
1 / 8646 |
0.0116% |
| Finnish |
0 / 6614 |
0% |
| Non-Finnish |
5 / 66462 |
0.00752% |
| Other |
0 / 904 |
0% |
| South Asian |
1 / 16510 |
0.00606% |
| Total MAF |
8 / 121048 |
0.00661% |
COSMIC
COSMIC Mutation ID = COSV50440436
COSMIC_FATHMM_PREDICTION = PATHOGENIC
COSMIC_MUTATION_SOMATIC_STATUS = true
gnomAD
gnomAD
Source: Genome / Exome
| Ethnicity |
Count / Number |
MAF |
| African |
1 / 24920 |
0.00401% |
| America/Latino |
0 / 35432 |
0% |
| Ashkenazi Jewish |
0 / 10368 |
0% |
| East Asian |
5 / 19950 |
0.0251% |
| Finnish |
0 / 25112 |
0% |
| Non-Finnish |
8 / 129028 |
0.0062% |
| Other |
0 / 7220 |
0% |
| South Asian |
1 / 30614 |
0.00327% |
| Korean |
0 / 3818 |
0% |
| Japanese |
0 / 152 |
0% |
| Other East Asian |
5 / 14422 |
0.0347% |
| Bulgarian |
0 / 2670 |
0% |
| Estonian |
0 / 4784 |
0% |
| North-Western European |
5 / 50774 |
0.00985% |
| Southern European |
0 / 11600 |
0% |
| Swedish |
2 / 26126 |
0.00766% |
| Other non-Finnish European |
1 / 33074 |
0.00302% |
| Total MAF |
15 / 282644 |
0.00531% |
Export Variant