Variant detail

mut_id 140 · c.3367C>T · p.Arg1123Cys

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Evidence at a glance

3
Linked patients
3
Patient-variant records
6
Linked references
2
Countries reported
cTTP (3)
Common phenotype
compound_heterozygous (2)
Common zygosity

Summary

Point missense_variant Pathogenic/Likely pathogenic Residue 1123 AlphaMissense key R1123C
HGVS
c.3367C>T
Protein change
p.Arg1123Cys
rsID
rs281875340
ClinVar ID
68816
GRCh38 coordinate
133455402
Location
exon 25
gnomAD AF
4.3411E-06
Domain
TSP type-1 8
Gene
ADAMTS13

External links

dbSNP ClinVar gnomAD

References

Inherited Thrombotic Thrombocytopenic Purpura Revealed by Recurrent Strokes in a Male Adult: Case Report and Literature Review
Authors: Beauvais D, Venditti L, Chassin O, Joly B, Ameri A, Boisseau P, Lambotte O, Coppo P, Veyradier A, Denier C.
Source: J Stroke Cerebrovasc Dis (2019)
Citation: J Stroke Cerebrovasc Dis. 2019 Jun;28(6):1537-1539. doi: 10.1016/j.jstrokecerebrovasdis.2019.03.011. Epub 2019 Mar 28.
PubMed: 30930238 · DOI: 10.1016/j.jstrokecerebrovasdis.2019.03.011
[Thrombotic thrombocytopenic purpura in a newborn]
Authors: Sudour H, Rouabah M, Mansuy L, Bordigoni P, Hascoet JM.
Source: Arch Pediatr (2007)
Citation: Arch Pediatr. 2007 Jan;14(1):39-42. doi: 10.1016/j.arcped.2006.10.016. Epub 2006 Nov 28.
PubMed: 17137768 · DOI: 10.1016/j.arcped.2006.10.016
[From gene to disease; congenital thrombotic thrombocytopenic purpura due to mutations in the ADAMTS13 gene]
Authors: Schiphorst RH, van de Kar NC, van den Heuvel LP.
Source: Ned Tijdschr Geneeskd (2003)
Citation: Ned Tijdschr Geneeskd. 2003 Dec 6;147(49):2422-4.
PubMed: 14694551
Application of high-throughput sequencing for hereditary thrombocytopenia in southwestern China
Authors: Zhang L, Yu J, Xian Y, Wen X, Guan X, Guo Y, Luo M, Dou Y.
Source: J Clin Lab Anal (2021)
Citation: J Clin Lab Anal. 2021 Aug;35(8):e23896. doi: 10.1002/jcla.23896. Epub 2021 Jul 8.
PubMed: 34237177 · DOI: 10.1002/jcla.23896
A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
Authors: Hunt R, Hettiarachchi G, Katneni U, Hernandez N, Holcomb D, Kames J, Alnifaidy R, Lin B, Hamasaki-Katagiri N, Wesley A, Kafri T, Morris C, Bouché L, Panico M, Schiller T, Ibla J, Bar H, Ismail A, Morris H, Komar A, Kimchi-Sarfaty C.
Source: Int J Mol Sci (2019)
Citation: Int J Mol Sci. 2019 Nov 15;20(22):5734. doi: 10.3390/ijms20225734.
PubMed: 31731663 · DOI: 10.3390/ijms20225734
Congenital late onset thrombotic thrombocytopenic purpura: a diagnostic challenge
Authors: Enjeti AK, Chapman K, Taylor PJ, Meldrum C.
Source: Pathology (2015)
Citation: Pathology. 2015 Oct;47(6):585-6. doi: 10.1097/PAT.0000000000000303.
PubMed: 26352112 · DOI: 10.1097/PAT.0000000000000303

Amino-acid property change

Residue substitution
R → C at 1123
AlphaMissense score
0.3685
Uncertain
CSV class: Amb
Hydrophobicity
hydrophilic → hydrophilic (unchanged)
Charge
postive → neutral
Polarity
polar → polar (unchanged)
Size
large → medium
Residue type
basic → Unknown
Typical protein position
surface → buried
Hydropathy index
-4.5 → 2.5
Molecular weight
174.2 → 121.2
Original residue details
R · arginine
code: Arg
hydro: hydrophilic
charge: postive
polarity: polar
size: large
type: basic
Variant residue details
C · cysteine
code: Cys
hydro: hydrophilic
charge: neutral
polarity: polar
size: medium
type:

Interactive AlphaFold structure

Interactive local 3D view of the AlphaFold Q76LX8 ADAMTS13 structure.
Drag to rotate, shift-drag to move, and use the mouse wheel to zoom in and out. The default view shows the full ADAMTS13 structure, with residue 1123 highlighted in red.
AlphaFold Q76LX8 ADAMTS13 structure
Domain: TSP type-1 8
Domain colours match the homepage domain viewer.

Patient summary

Countries represented
Japan (2); Italy (1)
Phenotype
cTTP (3)
Zygosity
compound_heterozygous (2); homozygous (1)
Sex
female (2); male (1)
Pregnancy-related
no (2); unknown (1)
Triggers
unknown (1); infection (1); none (1)
Treatment
unknown (1); none (1); PI (1)
ADAMTS13 activity
n=3; median=3; range=0.5–6
Age of onset
n=3; median=3; range=1–6
Age of diagnosis
n=1; median=14; range=14–14
Platelet count
n=1; median=37; range=37–37

Variant fields

mut_syn_HGVS
c.3367C>T
cdna_numb_HGVS
3367
cdna_numb_legacy
3367
nt_change
C>T
n_bp
1
nuc_numb
3367
g_numb
g16
aa_numb_HGVS
1123
aa_numb_legacy
1123
aa_first
Arg
aa_last
Cys
aa_syn
p.Arg1123Cys
codon_first
CGT
codon_last
TGT
coordinate_GRCh38
133455402
gnomAD_AC
7
gnomAD_AN
1612504
gnomAD_AF
4.3411E-06
clinvar_id
68816
clinvar_classification
Pathogenic/Likely pathogenic
g_id
g16
g_name
ADAMTS13
comments
Pathogenic
refState
complete
ref_id
71, 163, 179, 205, 214, 233

Patients linked by mut_id

patient_id mut_id compound_partner_mut_id ref_id phenotype zygosity country sex age_of_onset age_of_diagnosis ad13_activity platelet_count pregnancy_related triggers treatment
143 140 168 214 cTTP compound_heterozygous Japan female <6 unknown <0.5 unknown unknown unknown unknown
199 140 . 233 cTTP homozygous Italy male 3 unknown <6 37 no infection none
273 140 168 179 cTTP compound_heterozygous Japan female <1 14 <3 unknown no none PI