Glanzmann Thrombasthenia in Pakistani Patients: Identification of 7 Novel Pathogenic Variants in the Fibrinogen Receptor αIIbβ3
Abstract
:1. Introduction
2. Patients and Methods
2.1. Sample Collection and Biochemical Analysis
2.2. Platelet Aggregregometry Analyses
2.3. Flow Cytometry Analyses
2.4. Extraction, Amplification and Sequencing of Genomic DNA
3. Results
4. Discussion
4.1. Novel Variants in ITGA2B Classified as Pathogenic (Class 5) Because of Serious Consequences
4.2. Novel Variants in ITGA2B Classified as likely Pathogenic or as Variant of Uncertain Significance with Pathogenic Prediction
4.3. Variants in ITGA2B Which Have Been already Reported
4.4. Variants in ITGB3
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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ID | Age (yrs) | Gender F/M | CS | BS | Platelet Count 109/L | Platelet Aggregation Studies: in % of Aggregation [Normal Max. Agg: >55%] | Flow Cytometric Analysis | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ADP [2.25 µM] | Coll [4 µg/mL] | Epi [5 µM] | Risto [0.5 mg/mL] | AA [500 µg/mL] | CD41 (αIIb) [MFI] (56–75%) | CD61 (β3) [MFI] (57–73%) | CD42a [MFI] (53–69%) | CD42b [MFI] (52–75%) | ||||||
1 | 14 | M | Y | 8 | 313 | 4 | 2 | 4 | 55 | 5 | 0 | 0 | 52 | 54 |
2 | 1.5 | F | Y | 7 | 525 | 2 | 4 | 3 | 51 | 3 | 1 | 23 | 86 | 73 |
3 | 30 | M | N | 9 | 189 | 4 | 3 | 3 | 59 | 2 | 47 | 73 | 74 | 74 |
4_F1 | 18 | M | Y | 8 | 254 | 3 | 3 | 5 | 53 | 3 | 0 | 0 | 75 | 62 |
5_F1 | 22 | F | Y | 11 | 338 | 4 | 3 | 5 | 55 | 5 | 0 | 0 | 61 | 54 |
6 | 20 | M | Y | 10 | 186 | 2 | 5 | 4 | 58 | 3 | 4 | 9 | 85 | 77 |
7 | 18 | M | Y | 10 | 124 | 3 | 2 | 5 | 60 | 4 | 0 | 0 | 83 | 55 |
8 | 15 | F | Y | 14 | 166 | 4 | 3 | 4 | 52 | 2 | 0 | 0 | 71 | 57 |
9 | 6 | F | Y | 14 | 247 | 5 | 5 | 5 | 55 | 4 | 0 | 0 | 73 | 69 |
10_F2 | 20 | M | Y | 10 | 185 | 5 | 4 | 5 | 56 | 4 | 1 | 0 | 80 | 61 |
11_F2 | 23 | F | Y | 11 | 150 | 3 | 5 | 4 | 57 | 3 | 0 | 0 | 72 | 62 |
12 | 26 | M | N | 7 | 128 | 2 | 4 | 4 | 60 | 4 | 0 | 0 | 60 | 67 |
13_F3 | 21 | M | Y | 7 | 319 | 3 | 3 | 3 | 51 | 5 | 0 | 0 | 69 | 75 |
14_F3 | 28 | F | Y | 12 | 368 | 3 | 4 | 3 | 62 | 5 | 0 | 0 | 76 | 55 |
15 | 22 | M | Y | 14 | 358 | 3 | 5 | 4 | 64 | 3 | 51 | 17 | 90 | 71 |
16 | 23 | M | Y | 9 | 128 | 3 | 4 | 4 | 55 | 5 | 1 | 0 | 77 | 59 |
17 | 32 | M | Y | 6 | 268 | 3 | 2 | 3 | 55 | 3 | 81 | 83 | 83 | 75 |
18_F4 | 3.5 | M | Y | 7 | 302 | 3 | 5 | 3 | 55 | 3 | 88 | 85 | 83 | 79 |
19_F4 | 7 | F | Y | 9 | 310 | 4 | 5 | 5 | 55 | 3 | 76 | 73 | 81 | 70 |
20 | 7 | F | Y | 8 | 297 | 3 | 3 | 5 | 55 | 5 | 70 | 65 | 78 | 72 |
Pt. | Exon | Allele | Nucleotide/ Amino Acid | MAF gnomAD/dbSNP rsId | In Silico PP | Remarks |
---|---|---|---|---|---|---|
1 | Donor splice site of intron 1 | 2 | c.188 + 1G > A/ Predicted change at donor site 1 bps upstream: −100% | no | MaxEnt:−100.0% NNSPLICE:−100.0% SSF:−100.0% | Novel |
2 | Acceptor splice site of intron 4 | 2 | c.575–2A > T/ Predicted change at acceptor site 2 bps downstream: −100% | no | MaxEnt:−100.0% NNSPLICE:−100.0% SSF:−100.0% | Novel |
3 | 6 | 2 | c.659A >G/p.Tyr220Cys | MAF 0.00079%, rs1355838837 | SIFT/MutTaster: D PolyPhen 2: Probably damaging | Reported compound heterozygous [11]; ClinGen Exp.#: LP |
4_F, 15_F1 | 9 | 2 | c.857T > A/ p.Val286Asp | no | SIFT/MutTaster: D PolyPhen 2: Possibly Damaging | Reported [12] |
6 | 11 | 1 | c.989A > T/ p.Asn330Ile | no | SIFT/MutTaster: D PolyPhen 2: Probably damaging | Novel |
12 | 1 | c.1028T > C/ p.Leu343Pro | no | SIFT/MutTaster: D PolyPhen 2: Probably damaging | Reported [4]; ClinGen Exp.#: LP | |
7 | 13 | 2 | c.1355T > G/ p.Leu452Arg | MAF 0.00079%, rs775251867 | SIFT/MutTaster: D PolyPhen 2: Probably damaging | Novel |
8 | 14 | 2 | c.1423C > T/ p.Gln475* | no | Novel | |
9 | 29 | 2 | c.3001_3010dup/ p.Val1004Alafs*35 | no | Novel |
Pt. | Exon | Allele | Nucleotide/ Amino Acid | MAF gnomAD dbSNP rsId | In Silico PP | Remarks |
---|---|---|---|---|---|---|
10_F2 | 4 | 1 | c.383T > G/p.Ile128Ser | no | SIFT: D MutTaster: 50/50 del/benign, PolyPhen2: Possibly Damaging | VUS |
4 | 2 | c.422A > G/p.Tyr141Cys | no | SIFT/MutTaster: D PolyPhen 2: Probably damaging | Reported [13], ClinGen Exp.§: VUS | |
11_F2 | 4 | 2 | c.422A > G/p.Tyr141Cys | no | SIFT/MutTaster: D PolyPhen 2: Probably damaging | Reported [13], ClinGen Exp.§: VUS |
12 | 4 | 2 | c.422A > G/p.Tyr141Cys | no | SIFT/MutTaster: D PolyPhen 2: Probably damaging | Reported [13], ClinGen Exp.§: VUS |
13_F3 14_F3 | 4 | 2 | c.428T > G/p.Leu143Trp | MAF 0.00397%, rs121918452 | SIFT/MutTaster: D PolyPhen 2: Probably damaging | Reported [14,15], ClinGen Exp.#: LP |
15 | 4 | 2 | c.428T > C/p.Leu143Ser | no | SIFT/MutTaster: D PolyPhen 2: Probably damaging | Novel |
17 | 3 | 1 | c.197T > G/p.Leu66Arg | MAF 0.35293%, rs36080296 | SIFT/MutTaster: D PolyPhen 2: Probably damaging | ClinGen Exp.§: VUS |
Flow Cytometric Analysis | ||||||
---|---|---|---|---|---|---|
Patient/ Proband | CD41 (αIIb) [MFI] (56–75%) | CD61 (β3) [MFI] (57–73%) | Allele | Nucleotide | Amino Acid | Remarks |
Pt.4 | 0 | 0 | 2 | c.857T > A | p.Val286Asp | Reported [12], but no phenotype description |
Pt.5 | 0 | 0 | 2 | |||
Father | 54 | 63 | 1 | |||
Mother | 64 | 66 | 1 | |||
Pt.8 | 0 | 0 | 2 | c.1423C > T | p.Gln475* | Novel |
Mother | 59 | 60 | 1 | |||
Sibling 1 | 58 | 62 | 1 | |||
Sibling 2 | 77 | 75 | 2 | WT |
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Siddiqi, M.Y.J.; Boeckelmann, D.; Naz, A.; Imran, A.; Ahmed, S.; Najmuddin, A.; Zieger, B. Glanzmann Thrombasthenia in Pakistani Patients: Identification of 7 Novel Pathogenic Variants in the Fibrinogen Receptor αIIbβ3. Cells 2023, 12, 213. https://doi.org/10.3390/cells12020213
Siddiqi MYJ, Boeckelmann D, Naz A, Imran A, Ahmed S, Najmuddin A, Zieger B. Glanzmann Thrombasthenia in Pakistani Patients: Identification of 7 Novel Pathogenic Variants in the Fibrinogen Receptor αIIbβ3. Cells. 2023; 12(2):213. https://doi.org/10.3390/cells12020213
Chicago/Turabian StyleSiddiqi, Muhammad Younus Jamal, Doris Boeckelmann, Arshi Naz, Ayisha Imran, Shariq Ahmed, Akbar Najmuddin, and Barbara Zieger. 2023. "Glanzmann Thrombasthenia in Pakistani Patients: Identification of 7 Novel Pathogenic Variants in the Fibrinogen Receptor αIIbβ3" Cells 12, no. 2: 213. https://doi.org/10.3390/cells12020213
APA StyleSiddiqi, M. Y. J., Boeckelmann, D., Naz, A., Imran, A., Ahmed, S., Najmuddin, A., & Zieger, B. (2023). Glanzmann Thrombasthenia in Pakistani Patients: Identification of 7 Novel Pathogenic Variants in the Fibrinogen Receptor αIIbβ3. Cells, 12(2), 213. https://doi.org/10.3390/cells12020213