| Literature DB >> 30266296 |
Werner F Blum1, Jürgen Klammt2, Serge Amselem3, Heike M Pfäffle2, Marie Legendre3, Marie-Laure Sobrier3, Marie-Pierre Luton3, Christopher J Child4, Christine Jones5, Alan G Zimmermann6, Charmian A Quigley7, Gordon B Cutler8, Cheri L Deal9, Jan Lebl10, Ron G Rosenfeld11, John S Parks12, Roland W Pfäffle2.
Abstract
Entities:
Keywords: Genetics; Growth hormone deficiency; Hypopituitarism; Pituitary; Short stature
Mesh:
Substances:
Year: 2018 PMID: 30266296 PMCID: PMC6197701 DOI: 10.1016/j.ebiom.2018.09.026
Source DB: PubMed Journal: EBioMedicine ISSN: 2352-3964 Impact factor: 8.143
Number and percentage of patients with mutations.
| Gene | All in study | IGHD | CPHD | Unknown | Patients tested | Mutations in tested patients |
|---|---|---|---|---|---|---|
| n (%) | n (%) | n (%) | n (%) | n (%) | n (%) | |
| All studied | 917 (100.0%) | 475 (100.0%) | 415 (100.0%) | 27 (100.0%) | ||
| All without mutation | 825 (90.0%) | 444 (93.5%) | 354 (85.3%) | 27 (100.0%) | ||
| All with mutation | 92 (10.0%) | 31 (6.5%) | 61 (14.7%) | 0 (0.0%) | ||
| 26 (2.8%) | 23 (4.8%) | 3 (0.7%) | 0 (0.0%) | 531 (57.9%) | 26 (4.9%) | |
| 5 (0.5%) | 5 (1.1%) | 0 (0.0%) | 0 (0.0%) | 526 (57.4%) | 5 (1.0%) | |
| 1 (0.1%) | 0 (0.0%) | 1 (0.2%) | 0 (0.0%) | 123 (13.4%) | 1 (0.8%) | |
| 2 (0.2%) | 0 (0.0%) | 2 (0.5%) | 0 (0.0%) | 417 (45.5%) | 2 (0.5%) | |
| 5 (0.5%) | 0 (0.0%) | 5 (1.2%) | 0 (0.0%) | 396 (43.2%) | 5 (1.3%) | |
| 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 224 (24.4%) | 0 (0.0%) | |
| 2 (0.2%) | 0 (0.0%) | 2 (0.5%) | 0 (0.0%) | 393 (42.9%) | 2 (0.5%) | |
| 49 (5.3%) | 1 (0.2%) | 48 (11.6%) | 0 (0.0%) | 418 (45.6%) | 49 (11.7%) | |
| 2 (0.2%) | 2 (0.4%) | 0 (0.0%) | 0 (0.0%) | 445 (48.5%) | 2 (0.4%) |
Patients are split by pituitary secretory status (isolated GHD [IGHD] or combined pituitary hormone deficiencies [CPHD]).
Pituitary secretory status could not be unequivocally assigned.
Mutations identified within the study.
| no. | cDNA change | Protein change (shown or predicted) | Type of variation | Zygosity | Ref. | Genotype frequency [% (n)] | Minor allele frequency (%) this study (n); [1kG/ESP/ExAC/gnomAD] | Predicted impact PolyPhen/SIFT/MutationTaster |
|---|---|---|---|---|---|---|---|---|
| 1 | 6.7 kB gene deletion | p.0 | Del | Ho | [ | 0.407(2) | 0.407 (4); [n.a.] | n.a. |
| 2 | 7.0 kB gene deletion | p.0 | Del | Ho | [ | 0.203 (1) | 0.203 (2); [n.a.] | n.a. |
| 3 | c.178G>A | p.Ala60Thr (see text) | missense | He | Novel | 0.203 (1) | 0.102 (1); [ – /– /– /– ] | Benign /benign /benign |
| 4 | c.275A>G | p.Glu92Gly (see text) | missense | He | Novel | 0.203 (1) | 0.102 (1); [ – /– /– /– ] | Damaging /damaging /benign |
| 5 | c.291+1G>A | p.Glu58_Ser97del | SD | He | [ | 2.033 (10) | 1.016 (10); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 6 | c.291+2T>C | p.Glu58_Ser97del | SD | He | [ | 0.203 (1) | 0.102 (1); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 7 | c.291+3G>C | p.Glu58_Ser97del | SD | He | Novel | 0.407 (2) | 0.203 (2); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 8 | c.291+5G>A | p.Glu58_Ser97del | SD | He | [ | 0.203 (1) | 0.102 (1); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 9 | c.292-37_292-16del | p.Glu58_Ser97del | BS | He | Novel [ | 0.203 (1) | 0.102 (1); [ – /– /– /– ] | n.a. /n.a. /benign |
| 10 | c.499C>T | p.Gln167Ter | nonsense | He | Novel | 0.203 (1) | 0.102 (1); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 11 | c.57+1G>T | p.? | SD | cHe[S5:5] | Novel | 0.204 (1) | 0.102 (1); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 12 | c.214G>T | p.Glu72Ter | nonsense | cHe17 | [ | 0.204 (1) | 0.102 (1); [ 0.02 /– /0.048 /0.019] | n.a. /n.a. /damaging |
| 13 | c.335G>A | p.Cys112Tyr | missense | cHe16 | Novel | 0.204 (1) | 0.102 (1); [ – /– /– /– ] | Damaging /benign /damaging |
| 14 | c.758C>T | p.Pro253Leu | missense | cHe15 | Novel | 0.204 (1) | 0.102 (1); [ – /– /– /– ] | Damaging /damaging /damaging |
| 15 | c.812+1G>A | p.? (see citation) | SD | cHe14 | [ | 0.204 (1) | 0.102 (1); [ – /– /8.2E–4 /4.1E–4] | n.a. /n.a. /damaging |
| 16 | c.1089_1093del | p.Leu364Phefs | Del-FS | cHe13 | [ | 0.204 (1) | 0.102 (1); [ – /0.024 /7.0E–3 /5.1E–3] | n.a. /n.a. /damaging |
| 17 | c.1102C>T | p.Gln368Ter | nonsense | cHe12 | Novel | 0.204 (1) | 0.102 (1); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 18 | c.1807_1810dup | p.His604Argfs | Ins-FS | He | Novel | 0.826 (1) | 0.413 (1); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 19 | c.385_386ins315 | p.? (see citation) | Ins-FS | Ho | Novel [ | 0.254 (1) | 0.254 (2); [ – /– /– /– ] | n.a. |
| 20 | c.479G>A | p.Arg160His | missense | dHe[S5:12] | [ | 0.270 (1) | 0.127 (1); [ – /– /– /1.1E–3] | Damaging /damaging /damaging |
| 21 | c.252-3C>G | p.? (see citation) | SA | cHe23 | Novel [ | 0.269 (1) | 0.134 (1); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 22 | c.287_288delinsTCCT | p.Gly96Valfs | Ins-Del-FS | Ho | Novel [ | 0.269 (1) | 0.269 (2); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 23 | c.353G>A | p.Cys118Tyr | Missense | cHe21 | Novel [ | 0.269 (1) | 0.134 (1); [ – /– /– /– ] | Damaging /damaging /damaging |
| 24 | c.629C>T | p.Ala210Val | Missense | Ho | Novel [ | 0.269 (1) | 0.269 (2); [ – /– /– /– ] | Damaging /damaging /damaging |
| 25 | c.672G>A | p.Trp224Ter | Nonsense | Ho | Novel [ | 0.269 (1) | 0.269 (2); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 26 | c.427C>T | p.Arg143Ter | nonsense | Ho | Novel | 0.271 (1) | 0.271 (2); [ – /– /– /– ] | n.a. /n.a. /damaging |
| 27 | gene deletion | p.0 | Del | Ho | [ | 0.255 (1) | 0.255 (2); [n.a.] | n.a. |
| 28 | c.150del | p.Arg53Aspfs | Del-FS | Ho, cHe32 | [ | 2.551 (10) | 1.403 (11); [ – /– /– /9.7E–3] | n.a. /n.a. /damaging |
| Ho: 0.255 (1) | ||||||||
| cHe: 2.296 (9) | ||||||||
| 29 | c.211C>T | p.Arg71Cys | missense | cHe32 | [ | 0.255 (1) | 0.128 (1); [ – /– /3.3E–3 /2.0E–3] | Damaging /damaging /damaging |
| 30 | c.217C>T | p.Arg73Cys | missense | Ho | [ | 0.510 (2) | 0.510 (4); [ – /– /8.3E–4 /7.2E–4] | Damaging /damaging /damaging |
| 31 | c.295C>T | p.Arg99Ter | nonsense | Ho, cHe32 | [ | 0.510 (2) | 0.383 (3); [ – /– /– /7.2E–4] | n.a. /n.a. /damaging |
| Ho: 0.255 (1) | ||||||||
| cHe: 0.255 (1) | ||||||||
| 32 | c.301_302del | p.Leu102Cysfs | Del-FS | Ho, cHe28,29,31 | [ | 7.908 (31) | 6.505 (51); [ – /0.072 /0.014 /0.018] | n.a. /n.a. /damaging |
| Ho: 5.102 (20) | ||||||||
| cHe: 2.806 (11) | ||||||||
| 33 | c.712_744dup | p.Ala238_Ala248dup | Ins (in frame) | X-Hem | [ | 0.233 (1) | 0.172 (1); [ – /– /– /– ] | n.a. /n.a. /benign |
Numbers of mutations and genotypes and corresponding percentages refer to kindreds. Mutations in bold = transitions at CpG sites. n.a. = not applicable.
BS = branch site affected (splicing); Del = deletion; ESE = exonic splicing enhancer affected; FS = frameshift; Ins = insertion; SA = splice acceptor site affected; SD = splice donor site affected.
Ho = homozygous; He = heterozygous; X-Hem = X-linked hemizygous; cHe = compound heterozygous; dHe = double heterozygous, the no. (1st column) of the co-occurring variant/s is shown as superscript; numbers in brackets refer to variants listed in Supplementary Table S5.
Citations for variants identified in this study and previously published elsewhere are shown as superscript.
For details see Supplementary Table S2.
GH1 p.Glu58_Ser97del results from exon 3 skipping (17.5 k isoform).
Demographic data and phenotypic features of unpublished patients with previously undescribed (novel) mutations.⁎
| Pat. | Genotype (allele 1 /allele 2) | Inheritance (allele 1/allele 2) | Nationality | Sex | Mother's height (SDS) | Father’s height (SDS) | BL age (y) | Pre-HV (SDS) | BL Ht (SDS) | Max. GH peak (μg/L) | Additional pit. hormone deficiencies | Reported hypothalamic-pituitary morphology and other anomalies |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | c.[499C>T];[?] | ND /ND | Russia | F | ND | ND | 13.1 | −1.4 | −3.4 | 1.5 | ||
| p.[Q167 | ||||||||||||
| B | c.[178G>A];[=] | Ma /ND | Spain | M | −3.7 | −0.8 | 9.2 | ND | −0.4 | 4.7 | ADH | Histiocytosis |
| p.[A60T];[A60=] | ||||||||||||
| C | c.[291+3G>C];[=] | ND /ND | Germany | M | −0.1 | −0.1 | 1.7 | −2.7 | −4.2 | 0.2 | Acromicria | |
| p.[E58_S97del];[E58_S97=] | ||||||||||||
| D | c.[291+3G>C];[=] | ND /ND | Belgium | M | 2.3 | 1.1 | 1.3 | ND | −4.6 | 0.7 | Prominent forehead | |
| p.[E58_S97del];[E58_S97=] | ||||||||||||
| E1 (index) | c.[275A>G];[=] | Ma /Pa | France | M | −1.4 | 1.0 | 1.7 | −1.7 | −3.4 | 5.9 | Prominent forehead | |
| p.[E92G];[E92=] | ||||||||||||
| E2 (brother) | c.[275A>G];[=] | Ma /Pa | France | M | −1.4 | 1.0 | 3.2 | −2.7 | −3.3 | 3.8 | Prominent forehead | |
| p.[E92G];[E92=] | ||||||||||||
| E3 (cousin) | c.[275A>G];[=] | Ma /Pa | France | M | −1.9 | −0.7 | 2.1 | −1.7 | −3.1 | 2.7 | Prominent forehead | |
| p.[E92G];[E92=] | ||||||||||||
| F | c.[1102C>T];[214G>T] | Ma /ND | Thailand | M | −0.4 | −1.2 | 7.4 | −4.0 | −4.0 | <0.5 | Trunk obesity | |
| p.[Q368 | ||||||||||||
| G | c.[758C>T];[812+1G>A] | Ma /Pa | Thailand | M | −0.2 | −1.0 | 6.9 | ND | −4.8 | 0.7 | PH | |
| p.[P253L];[(see ref. 27)] | ||||||||||||
| H | c.[335G>A];[1089_1093del] | Ma /Pa | Australia | F | −1.7 | −1.0 | 5.5 | ND | −3.9 | 0.3 | Mild jaundice | |
| p.[C112Y];[L364Ffs | ||||||||||||
| I1 (index) | c.57+1G>T(;)177G>C | ND /ND | USA | M | −0.1 | 0.5 | 7.8 | −6.2 | −4.1 | 1.1 | ||
| p.(unknown)(;)W59C | ||||||||||||
| I2 (sister) | c.57+1G>T(;)177G>C | ND /ND | USA | F | −0.1 | 0.5 | 5.4 | −3.2 | ND | 1.3 | ||
| p.(unknown)(;)W59C | ||||||||||||
| J | c.[1807_1810dupGTGC];[=] | Ma /ND | India | M | −0,9 | −1,6 | 6.2 | ND | −3.8 | 0.1 | TSH, ACTH | EPP, PH Hypoglycemia, micropenis, acromicria, late dentition, late closure of fontanelles, dry skin, trunk obesity |
| p.[H604Rfs | ||||||||||||
| K1 (index) | c.[427C>T];[427C>T] | Ma /Pa | India | F | −0,5 | −2,3 | 3.2 | ND | −10.8 | 0.1 | TSH | Hypoglycemia, prominent forehead, late dentition |
| p.[R143 | ||||||||||||
| K2 (sister) | c.[427C>T];[427C>T] | Ma /Pa | India | F | −0,5 | −2,3 | 2.0 | ND | −8.3 | 0.1 | TSH | |
| p.[R143 | ||||||||||||
For details of published patients with novel mutations identified in GeNeSIS see references in Table 2. BL = baseline; SDS = standard deviation score; Pre-HV = height velocity before start of GH treatment; Ht = height. Ma = maternal. Pa = paternal. F = female. M = male; ND = not determined; PH = pituitary hypoplasia; EPP = ectopic posterior pituitary.
Baseline characteristics of patients with GH deficiency with or without mutations.
| Parameter | With mutation | Without mutation | P | ||
|---|---|---|---|---|---|
| n | Mean ± SD | n | Mean ± SD | ||
| Chronological age (y) | 90 | 5.7 ± 4.2 | 811 | 7.3 ± 4.7 | 0.004 |
| Bone age SDS | 54 | −3.7 ± 2.0 | 487 | −2.7 ± 1.8 | <0.001 |
| Height SDS | 74 | −4.1 ± 2.2 | 734 | −2.9 ± 1.5 | <0.001 |
| Target height SDS | 87 | −0.2 ± 1.0 | 748 | −0.5 ± 1.0 | 0.013 |
| Height SDS – target height SDS | 70 | −4.0 ± 2.0 | 674 | −2.4 ± 1.6 | <0.001 |
| Height velocity SDS | 35 | −2.3 ± 2.0 | 365 | −1.5 ± 1.9 | 0.020 |
| BMI SDS | 75 | −0.6 ± 2.2 | 686 | −0.7 ± 2.0 | 0.898 |
| Max. stimulated GH peak (μg/L) | 85 | 1.1 (0.5; 2.1) | 699 | 3.8 (1.3; 6.8) | <0.001 |
| IGF-I SDS | 27 | −5.9 ± 3.5 | 285 | −3.4 ± 3.3 | <0.001 |
| IGFBP-3 SDS | 26 | −4.7 ± 3.0 | 271 | −1.5 ± 2.6 | <0.001 |
| Fasting glucose (mg/dL) | 23 | 65.4 ± 14.7 | 172 | 75.3 ± 15.9 | 0.005 |
P-value by ANOVA.
Because of skewed distribution values are provided as median (1st quartile; 3rd quartile); P-value for rank-transformed data. y = year; SDS = standard deviation score; BMI = body mass index.
Fig. 1Maximum GH peak in stimulation tests by chronological age in patients with mutations. If more than one test was performed in a patient, the overall highest peak is presented.
Fig. 2Baseline height and stimulated GH peak serum concentrations of patients with IGHD depend on the type of mutation.
(A) Mean ± SD of height SDS in patients (n = 21) and affected relatives (n = 12, framed symbols) with IGHD type I, type II and type III. IGHD type IA with a very severe phenotype was due to GH1 deletions (#1, and #2 in Table 2) while IGHD type IB with a less severe phenotype was due to GHRHR mutations (#11–17 in Table 2). IGHD type II resulted from GH1 mutations #3–8 in Table 2, and IGHD type III from a SOX3 mutation (#33). The difference between IGHD type I vs. types II and III was significant by ANOVA (P < .001). (B) Height SDS versus log2(maximum GH peak) in patients (n = 19) and relatives (n = 6) with IGHD types I, II, and III. Pearson correlation (r = 0.51, P = .0099) and non-linear regression fitting the log2 presentation of the X-axis (hatched line) were calculated using GraphPad Prism 5 software (GraphPad Software, La Jolla, CA). ESE = carriers of mutations affecting putative exonic splicing enhancers. Intronic = invariant and other intronic splice site mutations.
Fig. 3Growth response to GH treatment versus year of therapy. (A) Height SDS, (B) height SDS – target height SDS, (C) height velocity SDS, (D) annualized change in height SDS per year. Patients with mutation (circles, red) versus without mutation (squares, blue). The graphs show the data of the longitudinal four-year population with available height SDS at each time-point (N = 27 with a mutation, N = 213 without a mutation). Data are presented as mean ± SEM, P-values by year, ns = not significant.
Baseline characteristics and final height outcome of GH treated patients with or without mutations.
| Parameter | With mutation | Without mutation | P | ||
|---|---|---|---|---|---|
| n | Mean ± SD | n | Mean ± SD | ||
| Females/males | 24 | 8/16 (33%/67%) | 191 | 71/120 (37%/63%) | |
| Chronological age (y) at baseline | 24 | 7.4 ± 4.3 | 191 | 9.4 ± 4.2 | 0.029 |
| Height SDS at baseline | 24 | −4.1 ± 2.3 | 191 | −2.9 ± 1.2 | <0.001 |
| Target height SDS | 23 | −0.1 ± 1.2 | 179 | −0.7 ± 1.0 | 0.014 |
| Height SDS – target height SDS | 23 | −4.1 ± 2.1 | 179 | −2.3 ± 1.5 | <0.001 |
| Max. stimulated GH peak (μg/L) | 24 | 1.0 (0.5; 2.3) | 175 | 4.7 (1.9; 7.7) | <0.001 |
| GH dose at start (mg/kg/week) | 23 | 0.19 ± 0.06 | 181 | 0.20 ± 0.07 | 0.239 |
| Last reported GH dose (mg/kg/week) | 24 | 0.17 ± 0.07 | 186 | 0.21 ± 0.09 | 0.037 |
| Age at final height (y) | 24 | 18.5 ± 1.7 | 191 | 17.7 ± 2.5 | 0.144 |
| Years on GH therapy (y) | 24 | 10.7 ± 4.4 | 190 | 7.7 ± 4.0 | <0.001 |
| Final height SDS | 24 | −0.7 ± 1.7 | 191 | −0.9 ± 1.3 | 0.386 |
| Final height SDS – target height SDS | 23 | −0.6 ± 1.3 | 179 | −0.3 ± 1.1 | 0.160 |
| Final height SDS gain | 24 | 3.4 ± 1.4 | 191 | 2.0 ± 1.4 | <0.001 |
| Patients with final height SDS > −2 | 24 | 20 (83%) | 191 | 161 (84%) | |
Values are provided as mean ± SD unless otherwise specified.
P-value by ANOVA; bold = significant differences.
Values are provided as n (%).
Because of skewed distribution, values are provided as median (1st quartile, 3rd quartile); P-value for rank-transformed data.
Final height SDS – height SDS at baseline. y = year; SDS = standard deviation score.
Fig. 4Final growth outcome. Height SDS at baseline (blue), final height SDS (green) and change in height SDS from baseline to final height (red) in various GeNeSIS cohorts: Patients with and without mutation tested in the DNA Analysis Sub-study; organic GH deficiency (GHD) including patients with genetic defects, intracranial tumors, and abnormal pituitary development; idiopathic GHD; idiopathic short stature (ISS); short for gestational age (SGA); Turner syndrome (Turner); short-stature homeobox-containing gene deficiency (SHOX-D). D indicates GH dose (mg/kg/week), N indicates cohort size. Data are shown as mean + or – SEM. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)