Comprehensive Screening of Genetic Variants in the Coding Region of F8 in Severe Hemophilia A Reveals a Relationship with Disease Severity in a Colombian Cohort
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design
2.2. Sample Collection and Sequencing
2.3. Protein Structure Prediction
2.4. Statistical Analysis
3. Results
3.1. F8 Variants Identified in Study Participants
3.2. Relationship between F8 Identified Variants and Inhibitor Risk
3.3. Previously Unreported F8 Variants
3.4. Three-Dimensional Structure of the F8 Protein
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Patient Code | Gene | cDNA Variant NM_00132.4 (F8) | Exon | Protein Position | Variant Effect | ACMG Classification | Inhibitors | Affected Protein Domains |
---|---|---|---|---|---|---|---|---|
ISMG03 | F8 | c.6045G>A | exon 19 of 26 position 47 of 117 | p.(Trp2015Ter) | nonsense | Pathogenic | Without inhibitor | -F5/8 type A3(Plastocyanin-like 5) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG04 | F8 | c.5882G>A | exon 18 of 26 position 67 of 183 | p.(Trp1961Ter) | nonsense | Pathogenic | High response (8.0) | -F5/8 type A3(Plastocyanin-like 5) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG05 | F8 | c.6972C>A | exon 26 of 26 position 72 of 1961 | p.(Tyr2324Ter) | nonsense | Pathogenic | Without inhibitor | -F5/8 type C2 (partial: 2193-2345) |
ISMG06 | F8 | c.2724delT | exon 14 of 26 position 611 of 3106 | p.(Pro909HisfsTer15) | Frameshift | Pathogenic | Without inhibitor | -B (partial: 760-1667) -F5/8 type A3(Plastocyanin-like 5) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG07 | F8 | c.2724delT | exon 14 of 26 position 611 of 3106 | p.(Pro909HisfsTer15) | Frameshift | Pathogenic | Without inhibitor | -B (partial: 760-1667) -F5/8 type A3(Plastocyanin-like 5) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG08 | F8 | c.4296_4300delTTCTC | exon 14 of 26 position 2183-2187 of 3106 | p.(His1434SerfsTer6) | Frameshift | Pathogenic | Without inhibitor | -B (partial: 760-1667) -F5/8 type A3(Plastocyanin-like 5) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG09 | F8 | c.5447_5448dupGG | exon 16 of 26 before position 76 of 213 | p.(Gln1817GlyfsTer55) | Frameshift | Pathogenic | Without inhibitor | -F5/8 type A3(Plastocyanin-like 5) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG14 | F8 | c.670+1G>T | intron 5 of 25 position 1 of 2433 splicing, intronic) | p.? | Pathogenic | Without inhibitor | ||
ISMG17 | F8 | c.389-2A>G | intron 3 of 25 position 3823 of 3824 splicing, intronic) | p.? | Pathogenic | Without inhibitor | ||
ISMG19 | F8 | c.1795G>T | exon 12 of 26 position 43 of 151 | p.(Asp599Tyr) | Missense | Likely pathogenic | Without inhibitor | -F5/8 type A 2 (Plastocyanin-like 4) |
ISMG21 | F8 | c.3836G>A | exon 14 of 26 position 1723 of 3106 | p.(Arg1279Lys) | Missense | VUS | Without inhibitor | -F5/8 type B |
ISMG22 | F8 | c.1946G>C | exon 13 of 26 position 43 of 210 | p.(Cys649Ser) | Missense | Pathogenic | Without inhibitor | -F5/8 type A 2 (Plastocyanin-like 4) |
ISMG23 | F8 | c.6666G>A | exon 24 of 26 position 92 of 149 | p.(Trp2222Ter) | Nonsense | Pathogenic | Without inhibitor | -F5/8 type A3(Plastocyanin-like 5) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG25 | F8 | c.6721C>T | exon 24 of 26 position 147 of 149 | p.(Gln2241Ter) | Nonsense | Pathogenic | Low response (0.6) | -F5/8 type C 2 |
ISMG30 | F8 | c.298dupT | exon 3 of 26 before position 34 of 123 | p.(Tyr100LeufsTer2) | Frameshift | Pathogenic | Without inhibitor | -F5/8 type A 1 -F5/8 type A 2 -Region B -F5/8 type A 3 -F5/8 type C 1 -F5/8 type C 2 |
ISMG31 | F8 | c.2609delC | exon 14 of 26 position 496 of 3106 | p.(Pro870LeufsTer7) | Frameshift | Pathogenic | Without inhibitor | -B (partial: 760-1667) -F5/8 type A 3 (complete: 1713-2040) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG32 | F8 | c.298dupT | exon 3 of 26 before position 34 of 123 | p.(Tyr100LeufsTer2) | Frameshift | Pathogenic | High response (16.0) | -F5/8 type A 1 -F5/8 type A 2 -Region B -F5/8 type A 3 -F5/8 type C 1 -F5/8 type C 2 |
ISMG34 | F8 | c.2945dupA | exon 14 of 26 before position 833 of 3106 | p.(Asn982LysfsTer9) | Frameshift | Pathogenic | Without inhibitor | -B (partial: 760-1667) -F5/8 type A 3 (complete: 1713-2040) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG35 | F8 | c.298dupT | exon 3 of 26 before position 34 of 123 | p.(Tyr100LeufsTer2) | Frameshift | Pathogenic | Without inhibitor | -F5/8 type A 1 -F5/8 type A 2 -Region B -F5/8 type A 3 -F5/8 type C 1 -F5/8 type C 2 |
ISMG38 | F8 | c.5447_5448dupGG | exon 16 of 26 before position 76 of 213 | p.(Gln1817GlyfsTer55) | Frameshift | Pathogenic | Low response (1.0) | -F5/8 type A3(Plastocyanin-like 5) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
ISMG43 | F8 | c.4379delA | exon 14 of 26 position 2266 of 3106 | p.(Asn1460IlefsTer5) | Frameshift | Pathogenic | Without inhibitor | -B (partial: 760-1667) -F5/8 type A 3 (complete: 1713-2040) -F5/8 type C1 (complete: 2040-2188) -F5/8 type C2 (complete: 2193-2345) |
n (%) | |||
---|---|---|---|
Chain | Heavy | A1 | 3 (14.3%) |
A2 | 2 (9.5% | ||
B | 7 (33.3%) | ||
Light | A3 | 4 (19.0) | |
C1 | 0 (0.0) | ||
C2 | 3 (14.3%) | ||
Splicing | 2 (9.5%) | ||
Type of variants | Frameshift | 11 (52.4) | |
Missense | 3 (14.3%) | ||
Nonsense | 5 (23.8%) | ||
Splicing | 2 (9.5%) |
Variants | n (%) | Domain | Coding Impact |
---|---|---|---|
c.298dupT | 3 (14.3%) | A1 | Frameshift |
c.1795G>T | 1 (4.8%) | A2 | Missense |
c.1946G>C | 1 (4.8%) | A2 | Missense |
c.2724delT | 2 (9.5%) | B | Frameshift |
c.2609delC | 1 (4.8%) | B | Frameshift |
c.2945dupA | 1 (4.8%) | B | Frameshift |
c.3836G>A | 1 (4.8%) | B | Missense |
c.4296_4300delTTCTC | 1 (4.8%) | B | Frameshift |
c.4379delA | 1 (4.8%) | B | Frameshift |
c.5447_5448dupGG | 2 (9.5%) | A3 | Frameshift |
c.5882G>A | 1 (4.8%) | A3 | Nonsense |
c.6045G>A | 1 (4.8%) | A3 | Nonsense |
c.6666G>A | 1 (4.8%) | C2 | Nonsense |
c.6721C>T | 1 (4.8%) | C2 | Nonsense |
c.6972C>A | 1 (4.8%) | C2 | Nonsense |
c.389-2A>G | 1 (4.8%) | - | Splicing |
c.670+1G>T | 1 (4.8%) | - | Splicing |
Total | 21 (100%) |
Inhibitors | Variants (NM_000132.4) | Coding Impact | Chain (Light/Heavy) | Frequency (%) |
---|---|---|---|---|
Without inhibitors | See Table 1 | 17(81%) | ||
Low response | c.5447_5448dupGG (Exon 16) c.6721C>T (Exon 24) | Frameshift Nonsense | A3 C2 | 2 (9.5%) |
High response | c.5882G>A (Exon 18) c.298dupT (Exon 3) | Nonsense Frameshift | A3 A1 | 2 (9.5%) |
Total | 21 (100%) |
Inhibitors | |||
---|---|---|---|
Coding Impact | Yes | No | * p-Value |
Frameshift | 2 | 9 | 0.457 |
Missense | 0 | 3 | |
Nonsense | 2 | 3 | |
Splicing | 0 | 2 | |
Total | 4 | 17 |
Inhibitors | |||
---|---|---|---|
Chain Location | Yes | No | p-Value |
Heavy | 1 | 11 | 0.075 |
Light | 3 | 4 | |
Total | 4 | 17 |
Coding Impact | Cohort (%) | Gouw et al. (%) | Atik et al. (%) |
---|---|---|---|
Missense | 14 | 34 | 45 |
Nonsense | 24 | 23 | 25 |
Frameshift | 52 | 36 | 25 |
Splice variant | 10 | 7 | 5 |
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Sarmiento Doncel, S.; Peláez, R.G.; Lapunzina, P.; Corrales-Medina, F.F.; Díaz Mosquera, G.A.; Bonanad, S.; Cortes, J.M.; Cazalla, M.; Gallego, N.; Querol-Giner, F.; et al. Comprehensive Screening of Genetic Variants in the Coding Region of F8 in Severe Hemophilia A Reveals a Relationship with Disease Severity in a Colombian Cohort. Life 2024, 14, 1041. https://doi.org/10.3390/life14081041
Sarmiento Doncel S, Peláez RG, Lapunzina P, Corrales-Medina FF, Díaz Mosquera GA, Bonanad S, Cortes JM, Cazalla M, Gallego N, Querol-Giner F, et al. Comprehensive Screening of Genetic Variants in the Coding Region of F8 in Severe Hemophilia A Reveals a Relationship with Disease Severity in a Colombian Cohort. Life. 2024; 14(8):1041. https://doi.org/10.3390/life14081041
Chicago/Turabian StyleSarmiento Doncel, Samuel, Ronald Guillermo Peláez, Pablo Lapunzina, Fernando F. Corrales-Medina, Gina Alejandra Díaz Mosquera, Santiago Bonanad, Javier Mauricio Cortes, Mario Cazalla, Natalia Gallego, Felipe Querol-Giner, and et al. 2024. "Comprehensive Screening of Genetic Variants in the Coding Region of F8 in Severe Hemophilia A Reveals a Relationship with Disease Severity in a Colombian Cohort" Life 14, no. 8: 1041. https://doi.org/10.3390/life14081041