| Literature DB >> 35928686 |
Jun Chen1,2, Yifan Yang1, Binjie Liu1,2, Xiaoli Xie1, Wenjie Li1,3,4.
Abstract
Background and aims: Hermansky-Pudlak syndrome (HPS) is an autosomal recessive disorder characterized by oculocutaneous albinism (OCA) and platelet storage pool deficiency. The HPS-2 subtype is distinguished by neutropenia, and little is known about its periodontal phenotype in adolescents. AP3B1 is the causative gene for HPS-2. A 13-year-old Chinese girl presented to our department suffering from gingival bleeding and tooth mobility. Her dental history was otherwise unremarkable. Suspecting some systemic diseases as the underlying cause, the patient was referred for medical consultation, a series of blood tests, and genetic tests. In this case study, periodontal status and mutation screening of one HPS-2 case are presented.Entities:
Keywords: Hermansky-Pudlak syndrome type 2 (HPS-2); adaptor protein complex 3 (AP3B1); genetics; juvenile; periodontitis
Year: 2022 PMID: 35928686 PMCID: PMC9343695 DOI: 10.3389/fped.2022.914243
Source DB: PubMed Journal: Front Pediatr ISSN: 2296-2360 Impact factor: 3.569
Figure 1Intraoral and facial photo (July 12, 2021): (A–I) The gums were extensively red and swollen. Abduction and displacement of maxillary anterior teeth. (J) The proband has blonde hair and whole-body skin whiteness.
Figure 2The proband's periodontal chart at the initial consultation.
Figure 3(A) Panoramic radiograph of the proband. (B–D) 3D Volumetric reconstructive cone-beam computed tomographic (CBCT) images of the whole mouth from different directions. (E–G) Alveolar bones of teeth #12, #11, and #26 were absorbed to the root apex.
Figure 4(A–D) Morphological analysis of platelets by platelet transmission electron microscopy (PTEM) shows multiple empty sacks (yellow arrows) in the proband's platelets without dense granules. Occasionally, abnormally dense granules with irregular shapes, decreased the content density and increased clear space (blue arrow). The platelet lysosomes (red arrow) increase in volume. Indicated magnification: (A) 10kx, (B) 10kx, (C) 30kx, (D) 20kx.
Eight heterozygous variants in six genes identified by whole-exome sequencing (WES) in the proband.
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| WDTC1 | c.1468+22G>A | – | – | – | 0.0113818 | 0.013 | 0.0144884 | – | |
| LAMP1 | c.112G>C | D | B | D | – | 1.653e-05 | 2.40429e-05 | – | pm2 |
| LAMP1 | c.562+4G>A | – | – | – | 0.00319489 | 0.0009225 | 0.000821249 | – | pp3 |
| SP6 | c.482T>C | D | B | T | – | 2.523e-05 | 1.12408e-05 | – | pm2 bp4 |
| AP3D1 | c.906+9C>T | – | – | – | 0.000599042 | 0.0002106 | 0.000183248 | 617050 | pm2 |
| AP3B1 | c.763C>T | A | – | – | – | – | – | 608233 | pvs1 pm1 pm2 pp3 |
| VPS33A | c.1165-50_1165-47del | – | – | – | – | – | – | 617303 | pm2 pm3_supporting |
| AP3B1 | c.53_56dup | – | – | – | – | – | – | 608233 | pvs1 pm2 |
MutationTaster_pred: A: disease_causing_automatic; D: disease_causing; N: polymorphism; P: polymorphism_automatic.
Polyphen2_HVAR_pred: D: Probably damaging (≥0.957), P: Possibly damaging (0.453 ≤ pp2_hdiv ≤ 0.956); B: Benign(pp2_hdiv ≤ 0.452).
SIFT_pred: D: Deleterious (sift ≤ 0.05); T: tolerated (sift > 0.05).
1000g2015aug_all: Allele frequency of the mutated base at this mutation locus in all populations of the 1000 Genomes Project.
ExAC_ALL: ExAC_ALL Database allele frequency of the mutated base at this variant locus in all populations.
gnomAD_exome_ALL: Allele frequencies of this variant in all populations of the gnomAD exon database.
phenotype_omim: This mutation corresponds to the OMIM number phenotype in the OMIM database.
ACMG: pathogenic: PVS1>PS1>…>PS4>PM1-6>PP1-5; benign: BA1>BS1-4>BP1-7. PVS, pathogenic very strong; PS, pathogenic strong; PM, pathogenic moderate; PP, pathogenic supporting; BA, benign strong; BP, benign supporting.
Figure 5(A) The pedigree contains three family members and two generations of Hermansky-Pudlak syndrome type 2 (HPS-2) (I1, I2, II1). The square represents the male, and the circle represents the female. The filled circle (arrow) represents the proband. A half-filled square or circle represents the carrier. (B) Sequence Chromatograms show the compound heterozygous mutations (c.763C>T: p.Q255*) and (c.53_56dup: p.E19Dfs*21) in the AP3B1 gene.
Reported AP3B1 pathogenic gene variants causing Hermansky-Pudlak syndrome type 2 (HPS-2).
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| c.2T > G | p.Met1Arg | M/90m | NA | ( |
| c.60 delG (*) | p.L20fsX41 | NA/1.25y, 2y | NA | ( |
| c.155_158delAGAG | p.Glu52Alafs*11 | M/NA | NA | ( |
| c.177delA | p.Lys59Asnfs*5 | M/52y | NA | ( |
| c.205T > C | p.Leu102Pro | NA/11y | NA | ( |
| c.716G > A | p.Trp239* | F/1m | NA | ( |
| c.904A > T | p.Arg302* | M/2y | Recurrent oral thrush | ( |
| c.1063_1064delCAinsSTATCAATATCg | p.Gln355Tyrfs*6 | Pt1: F/7y, Pt2:M/4yb | NA | ( |
| c.1095+5G > A | IVS10+5G>A | M/3y | Gingivitis, gum bleeding, excessive bleeding with dental procedures | ( |
| c.1168–1G > Cc | IVS11–1G>C | M/27y, M/22y | NA | ( |
| c.1473+6T > C | IVS14+6T>C | NA | NA | ( |
| c.1525C > Te | p.Arg509* | M/14y | Gingivitis | ( |
| c.1619dupG | p.Ala541Serfs*25 | NA | NA | ( |
| g.del8168-bp | del exon 15 | M/15y, M/21y | Pt2: aggressive periodontitis# | ( |
| g.del1872-bp | del exon 15 | F/14y | NA | ( |
| del exon 16 | – | NA/16y | NA | ( |
| c.1739T > G*d | p.Leu580Arg | M/27y, M/22y | NA | ( |
| c.1754delT | p.Val585Glufs*6 | F/4m | NA | ( |
| c.1789dupAh | p.Ile597Asnfs*12 | Pt1: F/7y, Pt2:M/4y | NA | ( |
| c.1839_1842delTAGA | p.Asp613Glufs*38 | F/4ma | NA | ( |
| c.1975G > Tf | p.Glu659* | M/11y | Gingivitis | ( |
| c.2041G > T | p.Glu681* | NA/2y | NA | ( |
| g.del624-bp | p.Glu693Valfs*13 | F/NA | NA | ( |
| c.2546T > G | p.Leu849* | M/19y | NA | ( |
| c.2702C > G | p.Ser901Cys | M/12m | NA | ( |
| c.2770delC(*) | p.Leu924Pefs*3 | NA/2.5y, 11y | NA | ( |
| c.2944delC | p.Leu982Cysfs*19 | F/15y | NA | ( |
| c.3222_3223delTG(*) | p.Lys1076Asnfs*60 | NA/5y, 13y | NA | ( |
| Inv(5)p15.1-q14.1 | – | F/70m | NA | ( |
| c.188T > A | p.M63K p.L849X | F/1y | NA | ( |
| C.1363+1G > A | – | M/6m | NA | ( |
–, unreported; Pt, Patient.
*This mutation involves two patients with similar clinical manifestations and is described together.
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