Variant detail

mut_id 122 · c.2883del · p.Cys962Alafs*3

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Evidence at a glance

1
Linked patients
1
Patient-variant records
1
Linked references
1
Countries reported
cTTP (1)
Common phenotype
homozygous (1)
Common zygosity

Summary

Deletion Deletion Residue 962 AlphaMissense key C962A
HGVS
c.2883del
Protein change
p.Cys962Alafs*3
GRCh38 coordinate
133449804
Location
exon 23
Domain
TSP type-1 6
Gene
ADAMTS13

External links

gnomAD

References

Congenital ADAMTS-13 deficiency presenting as life-threatening thrombosis during pregnancy
Authors: Hasan F, Gupta A, Chandra D, Nityanand S.
Source: BMJ Case Rep (2021)
Citation: BMJ Case Rep. 2021 Aug 11;14(8):e239901. doi: 10.1136/bcr-2020-239901.
PubMed: 34380671 · DOI: 10.1136/bcr-2020-239901

Amino-acid property change

Residue substitution
C → A at 962
AlphaMissense score
0.8886
Likely pathogenic
CSV class: LPath
Hydrophobicity
hydrophilic → hydrophobic
Charge
neutral → neutral (unchanged)
Polarity
polar → nonpolar
Size
medium → small
Residue type
Unknown → aliphatic
Typical protein position
buried → buried (unchanged)
Hydropathy index
2.5 → 1.8
Molecular weight
121.2 → 89.1
Original residue details
C · cysteine
code: Cys
hydro: hydrophilic
charge: neutral
polarity: polar
size: medium
type:
Variant residue details
A · alanine
code: Ala
hydro: hydrophobic
charge: neutral
polarity: nonpolar
size: small
type: aliphatic

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 962 highlighted in red.
AlphaFold Q76LX8 ADAMTS13 structure
Domain: TSP type-1 6
Domain colours match the homepage domain viewer.

Patient summary

Countries represented
Saudi Arabia (1)
Phenotype
cTTP (1)
Zygosity
homozygous (1)
Sex
male (1)
Pregnancy-related
no (1)
Triggers
none (1)
Treatment
PI (1)
ADAMTS13 activity
Not available
Age of onset
n=1; median=1; range=1–1
Age of diagnosis
n=1; median=1; range=1–1
Platelet count
n=1; median=8; range=8–8

Variant fields

mut_syn_HGVS
c.2883del
cdna_numb_HGVS
2883
cdna_numb_legacy
2883
nt_change
Deletion
nuc_numb
2883
g_numb
g16
aa_numb_HGVS
962
aa_numb_legacy
962
aa_first
Cys
aa_last
Ala
aa_syn
p.Cys962Alafs*3
coordinate_GRCh38
133449804
g_id
g16
g_name
ADAMTS13
refState
complete
ref_id
40

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
12 122 . 40 cTTP homozygous Saudi Arabia male <1 <1 unknown 8 no none PI