| Literature DB >> 32801813 |
Gabriella de Medeiros Abreu1, Camila de Almeida Pereira Dias Soares1, Roberta Magalhães Tarantino2,3, Ana Carolina Proença da Fonseca1, Ritiele Bastos de Souza1, Maria de Fátima Carvalho Pereira4, Pedro Hernan Cabello1,5, Melanie Rodacki2, Lenita Zajdenverg2, Verônica Marques Zembrzuski1, Mário Campos Junior1.
Abstract
PURPOSE: The aim of this study was to sequence the coding region of the PAX4 gene in a Brazilian cohort with clinical manifestations of monogenic diabetes. PATIENTS AND METHODS: This study included 31 patients with autosomal dominant history of diabetes, age at diagnosis ≤40 years, BMI <30 kg/m2, and no mutations in GCK or HNF1A, HNF4A, and HNF1B. Screening of the PAX4 coding region was performed by Sanger sequencing. In silico algorithms were used to assess the potential impact of amino acid substitutions on protein structure and function. Additionally, PAX4-MODY family members and 158 control subjects without diabetes were analyzed for the identified mutation.Entities:
Keywords: MODY; PAX4; diabetes mellitus; monogenic diabetes; mutation
Year: 2020 PMID: 32801813 PMCID: PMC7399458 DOI: 10.2147/DMSO.S256858
Source DB: PubMed Journal: Diabetes Metab Syndr Obes ISSN: 1178-7007 Impact factor: 3.168
Figure 1Diagrammatic representation of PAX4 gene and protein domains. Pathogenic mutations described associated to diabetes mellitus are pointed in the figure and PAX4-MODY are show in bold. Electropherograms of PAX4 exon 4 wild type and p.Arg164Gln (c.491G>A) in the patient DM35. Alignment by Clustal W (1.81) of PAX4 gene across species are presented (below).
In silico Prediction of Missense Mutations Identified in PAX4 Gene
| Prediction Tool | Output | PAX4 – p.Arg164Gln | PAX4 – p.Arg133Trp | ||
|---|---|---|---|---|---|
| Score | Prediction | Score | Prediction | ||
| SIFT | <0.05 damaging/≥0.05 tolerated (score range: 0–1) | 0.01 | Damaging | 0.1 | Tolerated |
| PolyPhen-2_HVAR | Probably damaging, possibly damaging or benign (score range: 0 [benign] to 1 [damaging]) | 0.997 | Probably damaging | 0.123 | Benign |
| PolyPhen-2_HDIV | Probably damaging, possibly damaging, or benign (score range: 0 [benign] to 1 [damaging]) | 1.000 | Probably damaging | 0.829 | Possibly damaging |
| PROVEAN | <−2.5 deleterious/>−2.5 neutral (default score threshold: −2.5) | −3.04 | Deleterious | 1.19 | Neutral |
| Revel | >0.50 likely disease causing/<0.50 likely benign (score range: 0 to 1) | 0.871 | Likely disease causing | 0.318 | Likely benign |
| WS-SNPs&GO | >0.5 disease-associated (score range: 0 to 1) | 0.642 | Disease | 0.160 | Neutral |
| MutPred2 | General pathogenicity score: ≥0.50 (score range: 0 to 1) | 0.501 | Possibly pathogenic | 0.175 | Benign |
| SNAP | ≥1 effect (score range: −100 to 100) | 74 | Effect | 71 | Effect |
| Fathmm | Pathogenicity threshold: <0 | −4.12 | Damaging | −3.40 | Damaging |
| M-CAP | Pathogenicity threshold: >0.025 | 0.337 | Possibly pathogenic | * | * |
| CADD | >30 likely deleterious/<30 likely benign | 31 | Likely deleterious | 22 | Likely benign |
| Mutation Assessor | Score cutoff: 0.8 neutral and low impact/1.9 low impact and medium impact/3.5 medium impact and high impact | 3.615 | High | 0 | Neutral |
| Align-GVGD | C0 most likely neutral to C65 most likely deleterious (classifiers: C0 to C65) | C35 | Likely deleterious | C65 | Likely deleterious |
| PANTHER-PSEP | Length of time: >450 my probably damaging/450 my>time>200 my possibly damaging/<200 my probably benign | 1038 | Probably damaging | 30 | Probably benign |
| Mutation Taster | A. Disease causing: probably deleterious/D. disease causing automatic: deleterious/N. polymorphism: probably harmless/P. polymorphism automatic: harmless | A | Disease causing | N | Polymorphism |
| Total prediction tools = 15 | 15 = predicted to be harmful | 4 = predicted to be harmful | |||
Notes: *M-CAP scores not available for some alleles at Ch7:127,254,551 chromosome position. SIFT: , Polyphen: , PROVEAN: , Revel: , WS-SNP&GO: , MutPred2: , SNAP: , Fathnm: , MCAP: , CADD: , MutationAssessor: , Align GVGD: , PANTHER-PSEP: , MutationTaster: .
Abbreviation: my, millions of years.
Characterization of Mutations in PAX4 Gene Associated to Diabetes Mellitus
| Exon or Intron | Mutated Protein | Mutated DNA | Consequence | Acess Number | Clinvar | Domain | Functional Studies | Ref. |
|---|---|---|---|---|---|---|---|---|
| 1 | p.Arg31Leu | c.92G>A | Missense | rs115887120 | Likely-benign | PD | na | [ |
| 1 | p.Arg37Trp | c.109C>T | Missense | rs35155575 | Uncertain-significance, risk-factor | PD | Decreased transcriptional repress promoter function and decreased binding activity | [ |
| 2 | p.Arg52Cys | c.154C>T | Missense | rs770923465 | na | PD | na | [ |
| 3 | n.a | c.374_412del | Sequence alteration | rs1325888696 | na | PD | Loss of transcriptional repressor function | [ |
| 3 | p.Arg121Trp | c.361C>T | Missense | rs114202595 | Pathogenic | PD | Loss of transcriptional repressor function | [ |
| 3 | p.Arg133Trp | c.397C>T | Missense | rs2233578 | Benign/Likely benign, risk factor | Between PD and HD | Decreased transcriptional repress promoter function | [ |
| 4 | p.Arg164Trp | c.490C>T | Missense | rs121917718 | Pathogenic | HD | Decreased transcriptional repress promoter function | [ |
| 4 | p.Arg164Gln | c.491G>A | Missense | rs587780414 | na | HD | na | # |
| IVS7 | IVS7-1G>A (p.Gln250del) | c.748–1G>A | Splice acceptor variant | rs371715169 | Pathogenic | Between HD and RD | Decreased transcriptional repress promoter function | [ |
Note: #Mutation identified in this study.
Abbreviations: Ref, reference; PD, paired domain; HD, homeodomain; RD, repressor domain; na, not available.
Figure 2Pedigree of family 35. Filled black symbols, grey symbols, and empty symbols represent diabetic patients, impaired glucose tolerance individuals, and healthy individuals, respectively. The present age of the individuals are shown below the symbols in years (y), followed by age of diagnosis in years, and genotype. Genotypes are expressed by normal allele (N) and mutated allele (M); An arrow indicates the index case.
Clinical Features and Laboratory Parameters of the Family 35 Members
| Patient | III-2 | III-3 | III-4 | III-6 | III-8* | III-9 | IV-3 | IV-5 | IV-6 | IV-9 | IV-12 | IV-13 | IV-14 | IV-15 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gender | Female | Female | Female | Female | Female | Female | Female | Female | Female | Female | Female | Female | Female | Male |
| BMI (kg/m2) | 29.48 | 23.61 | 24.93 | 27.97 | 24.8 | 30.62 | 25.73 | 25.55 | na | 20.38 | na | na | 23.23 | 28.84 |
| Current age (years) | 56 | 54 | 53 | 52 | 45 | 39 | 27 | 35 | 29 | 26 | 17 | 14 | 19 | 15 |
| AAD (years) | 38 | 49 | 50 | 25 | 32 | 24 | – | – | – | – | – | – | – | – |
| FPG (mg/dl) | 128 | 101 | 93 | 256 | na | 169 | 84 | 80 | na | 80 | na | na | 68 | 86 |
| HbA1c (%) | 11.3 | 6 | 6.1 | 9.6 | na | 7.4 | 5.3 | 5.5 | na | 5.1 | na | na | 5.4 | 5.4 |
| Treatment | OAD | OAD | Diet | Insulin | Insulin | Insulin | – | – | – | – | – | – | – | – |
| Genotype | MN | MN | MN | NN | MN | MN | MN | MN | MN | NN | NN | MN | NN | NN |
Note: *Proband.
Abbreviations: BMI, body mass index (at admission); AAD, age at diagnosis; FPG, fasting plasma glucose; HbA1c, glycated hemoglobin; OAD, oral antidiabetic agent; Genotypes are expressed by normal allele (N) and mutated allele (M); na, not available; –, not applicable.
Clinical Characteristics of Patients with DM with Mutations in PAX4 Gene
| P | Sex | AAD | BMI | HbA1c | Treat. | Mutation | Segregation Study DM/NDM | Nº P (He;Ho) | Nº C (He;Ho) | Ethnic Group | DM Type | Ref. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | F | 43 | 29.4 | 7 | Diet | p.Arg121Trp | na | 200 (6;1) | 161 (0;0) | Japanese | T2 DM | [ |
| 2 | M | 49 | 26.7 | 6.1 | Diet | p.Arg121Trp | na | |||||
| 3 | M | 49 | 17.8 | 8.1 | OAD | p.Arg121Trp | na | |||||
| 4 | F | 47 | 32.4 | 6.8 | OAD | p.Arg121Trp | na | |||||
| 5 | M | 32 | 22 | 8.8 | OAD | p.Arg121Trp | na | |||||
| 6 | F | 25 | 21.8 | 8.2 | Ins | p.Arg121Trp | na | |||||
| 7 | F | 29 | 22.2 | 7.3 | Ins | p.Arg121Trp* | 1MN/2MN | |||||
| 8 | M | 47 | 26.5 | 13.8 | OAD | p.Arg133Trp* | na | 101 (27;4) | 355 (69;0) | West African | KPD | [ |
| 9 | M | 22 | 16.2 | 12.2 | OAD | p.Arg133Trp* | na | |||||
| 10 | M | 38 | 25.4 | 14.1 | OAD | p.Arg133Trp* | na | |||||
| 11 | M | 20 | 21.6 | 12.5 | OAD | p.Arg133Trp* | na | |||||
| 12 | M | 39 | 28.7 | 11.6 | Ins | p.Arg37Trp | na | 101 (1;0) | 255 (0;0) | West African | KPD | [ |
| 13 | F | 20 | na | na | OAD | p.Arg164Trp | 2 NN, 3 MN/. | 46 (1;0) | 344 (0;0) | Thai | MODY | [ |
| 14 | F | 44 | na | na | na | IVS7-1G>A | 1 MN/1NN | 46 (1;0) | 344 (0;0) | Thai | MODY | [ |
| 15 | M | 15 | 18.2 | 14.5 | Ins | c.374_412del | 1 MN/. | 1 (1;0) | 150 (0;0) | Japanese | MODY | [ |
| 16 | M | 14 | 23 | na | Ins, OAD | p.Arg31Leu | na | 56 (1;0) | 60 (0;0) | Indian | MODY | [ |
| 17 | F | 38 | 28.4 | 14 | Ins | p.Arg37Trp | na | 1 (1;0) | 0 | African | KPD | [ |
| 18 | M | 35 | 28.1 | 9.2 | OAD | p.Arg52Cys | na | 84 (1;0) | 0 | Malay | MODY | [ |
| 19 | F | 32 | 21.6 | na | Ins | p.Arg164Gln | 1 NN, 5MN/4 NN, 4 MN | 31 (1;0) | 158 (0;0) | Brazilian | MODY | # |
Notes: *Mutation in homozygous state; #Mutation identified in this study; DM includes patients with impaired glucose tolerance.
Abbreviations: P, patient; AAD, age at diagnosis (in years); BMI, body mass index (kg/m2); HbA1c, glycated hemoglobin (%); Treat., treatment; DM, diabetes mellitus; NDM, non-diabetic subjects; N°, Number; He, mutation in heterozygous; Ho, mutation in homozygous; C, controls; Ref, reference; F, female; M, male; OAD, oral antidiabetic agents; Ins, insulin; na, not available; NM, genotype mutated in heterozygous state; NN, genotype homozygous normal; T2 DM, type 2 diabetes mellitus; KPD, ketosis-prone diabetes; MODY, maturity-onset diabetes of the young.