Variant detail

mut_id 309 · c.1192C>T · p.Arg398Cys

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Evidence at a glance

4
Linked patients
4
Patient-variant records
7
Linked references
3
Countries reported
cTTP (4)
Common phenotype
compound_heterozygous (4)
Common zygosity

Summary

Point missense_variant Likely pathogenic Residue 398 AlphaMissense key R398C
HGVS
c.1192C>T
Protein change
p.Arg398Cys
rsID
rs376606652
ClinVar ID
1700239
GRCh38 coordinate
133433477
Location
exon 10
gnomAD AF
0.00000371
Domain
TSP type-1 1
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
The International Hereditary Thrombotic Thrombocytopenic Purpura Registry: key findings at enrollment until 2017
Authors: van Dorland HA, Taleghani MM, Sakai K, Friedman KD, George JN, Hrachovinova I, Knöbl PN, von Krogh AS, Schneppenheim R, Aebi-Huber I, Bütikofer L, Largiadèr CR, Cermakova Z, Kokame K, Miyata T, Yagi H, Terrell DR, Vesely SK, Matsumoto M, Lämmle B, Fujimura Y, Kremer Hovinga JA; Hereditary TTP Registry.
Source: Haematologica (2019)
Citation: Haematologica. 2019 Oct;104(10):2107-2115. doi: 10.3324/haematol.2019.216796. Epub 2019 Feb 21.
PubMed: 30792199 · DOI: 10.3324/haematol.2019.216796
Transfusion-dependent anaemia of undetermined origin: a distinctive syndrome in paediatric medical tourism
Authors: Lee AC.
Source: Ann Acad Med Singap (2012)
Citation: Ann Acad Med Singap. 2012 Jul;41(7):305-8.
PubMed: 22892608
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
Next-generation sequencing study finds an excess of rare, coding single-nucleotide variants of ADAMTS13 in patients with deep vein thrombosis
Authors: Lotta LA, Tuana G, Yu J, Martinelli I, Wang M, Yu F, Passamonti SM, Pappalardo E, Valsecchi C, Scherer SE, Hale W 4th, Muzny DM, Randi G, Rosendaal FR, Gibbs RA, Peyvandi F.
Source: J Thromb Haemost (2013)
Citation: J Thromb Haemost. 2013 Jul;11(7):1228-39. doi: 10.1111/jth.12291.
PubMed: 23648131 · DOI: 10.1111/jth.12291
PB1884 | Correlation between Phenotype-genotype versus in-silico Prediction of Novel and Known Disease-causing Variants in UpshawSchulman Syndrome Patients in a Single Institution of Argentina
Authors: J. Paiva1 ; A.I. Woods2 ; A. Kinen1 ; M.M. Casinelli1 ; A. Sanchez-Luceros
Source: ISTH 2020 (2020)
Citation: ISTH 2020
PubMed: ISTH 2020

Amino-acid property change

Residue substitution
R → C at 398
AlphaMissense score
0.8190
Likely pathogenic
CSV class: LPath
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 398 highlighted in red.
AlphaFold Q76LX8 ADAMTS13 structure
Domain: TSP type-1 1
Domain colours match the homepage domain viewer.

Patient summary

Countries represented
Japan (2); India (1); UK (1)
Phenotype
cTTP (4)
Zygosity
compound_heterozygous (4)
Sex
male (2); female (2)
Pregnancy-related
no (3); unknown (1)
Triggers
none (2); unknown (1); infection (1)
Treatment
unknown (2); PI (2)
ADAMTS13 activity
n=3; median=0.5; range=0.5–5
Age of onset
n=4; median=1; range=1–14
Age of diagnosis
n=1; median=2; range=2–2
Platelet count
n=2; median=8.5; range=7–10

Variant fields

mut_syn_HGVS
c.1192C>T
cdna_numb_HGVS
1192
cdna_numb_legacy
1192
nt_change
C>T
n_bp
1
nuc_numb
1192
g_numb
g16
aa_numb_HGVS
398
aa_numb_legacy
398
aa_first
Arg
aa_last
Cys
aa_syn
p.Arg398Cys
codon_first
CGC
codon_last
TGC
coordinate_GRCh38
133433477
gnomAD_AC
6
gnomAD_AN
1613584
gnomAD_AF
0.00000371
clinvar_id
1700239
clinvar_classification
Likely pathogenic
g_id
g16
g_name
ADAMTS13
comments
Likely pathogenic
refState
complete
ref_id
71, 72, 138, 205, 214, 245, 309, 332

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
151 309 336 214 cTTP compound_heterozygous Japan male <14 unknown <0.5 7 unknown unknown unknown
227 309 336 245 cTTP compound_heterozygous Japan male <1 2 <0.5 10 no infection PI
285 309 238 309 cTTP compound_heterozygous India female <1 unknown unknown unknown no none unknown
355 309 313 138 cTTP compound_heterozygous UK female <1 unknown <5 unknown no none PI