As a tertiary genetic counseling and prenatal diagnosis center, our center served 290 families with individuals suspected of rare monogenic diseases during the 4-year study, and 142 (nearly 50%) of those patients had GDD/ID. After excluding 13 patients for missing information, 18 patients for uncertain diagnosis and 3 patients who had pathogenic variants along with atypical manifestations that could not be explained by the variants, we considered a total of 108 subjects (Fig. 1).
1. Demographic features and diagnostic courses of 108 patients with rare monogenic GDD/ID
The 108 subjects came from 21 out of the 31 provinces and municipalities in mainland China. The numbers of ARID, ADID and XLID cases were 50 (46.3%), 40 (37.8%) and 18 (16.2%), respectively. The median age was 41 months (IQR, 25-78.5), and 67 (62%) participants were male. The median age of onset was 6 months (IQR, 3–12), ranging from the day of birth to 5 years and 10 months, and 81 (75%) participants had symptoms before 1 year. All participants presented GDD before 6 years of age, but GDD was not necessarily their first manifestations.
The median interval from disease onset to genetic diagnosis was 14.9 months (IQR, 6–48), ranging from 1 month to 12 years, and the median duration from genetic diagnosis to genetic counseling was 10 months (IQR, 4–23; range, 0-105). The median number of hospital referrals was 4 (IQR, 3–5; range, 1–10) (Table 1 and Supplement 1).
Table 1
| Total | AR | AD | XL | P value |
(N = 108) | (N = 50) | (N = 40) | (N = 18) |
Male: Female | 67: 41 | 37: 13 | 22: 18 | 8: 10 | 0.044 |
Age, median (IQR), m | 41 (25, 78.5) | 37 (19, 73) | 46 (28, 74) | 53 (27, 112) | |
Age of onset, median (IQR), m | 6(3, 12) | 5 (3,12.5) | 6 (2, 9.5) | 6 (3, 15) | 0.757 |
≤1 m, n (%) | 15 (13.9) | 7 (14.3) | 5 (13.2) | 3 (16.7) | 0.653 |
1m༜age ≤ 1y, n (%) | 66 (61.1) | 30 (61.2) | 27 (71.0) | 9 (52.9) | |
1y༜age ≤ 3y, n (%) | 21 (19.4) | 10 (20.4) | 6 (15.8) | 5 (29.4) | |
3y༜age ≤ 6y, n (%) | 2 (1.9) | 2 (4.0) | 0 (0) | 0 (0) | |
6y༜age ≤ 18y, n (%) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | |
Age of genetic diagnosis, median (IQR), m | 24 (14, 60) | 20 (14, 53) | 28 (15, 72) | 48 (14, 96) | 0.286 |
Interval from onset to genetic diagnosis, median (IQR), m | 14 .9(6, 48) | 12 (6, 33) | 21 (6, 60) | 39 (9, 88) | 0.166 |
≤6 m, n (%) | 28 (25.9) | 16 (34) | 9 (25.7) | 3 (23.1) | 0.651 |
6m༜t ≤ 1y, n (%) | 16 (14.8) | 9 (19.1) | 5 (14.3) | 2 (15.4) | |
1y༜t ≤ 3y, n (%) | 21 (19.4) | 11 (23.4) | 9 (25.7) | 1 (7.7) | |
3y༜t ≤ 5y, n (%) | 14 (13.0) | 6 (12.8) | 5 (14.3) | 3 (23.1) | |
༞5y, n (%) | 16 (14.8) | 5 (10.6) | 7 (20) | 4 (30.8) | |
Method of sequencing,n (%) | | | | | 0.967 |
Whole exome sequencing | 52 (48.1) | 25 (53.2) | 18 (50.0) | 9 (56.3) | |
Targeted exome sequencing | 45 (41.7) | 21 (44.7) | 17 (47.2) | 7 (43.8) | |
Sanger sequencing | 2 (1.9) | 1 (2.1) | 1 (2.8) | 0 (0) | |
Duration from diagnosis to genetic counseling, median (IQR), m | 10 (4, 23) | 9 (3, 23) | 16 (5.5, 24.5) | 11 (4, 19) | 0.506 |
Number of referrals, median (IQR) | 4 (3, 5) | 4 (2, 5) | 4 (3, 5) | 3 (2, 5) | 0.605 |
Abbreviation: AR, autosomal recessive; AD, autosomal dominant; XL, X-linked; IQR, interquartile range; m, months; y, years |
2. Clinical Characteristics
Of the 108 subjects, 7 (7.8%) had mild GDD/ID, and the other 83 (92.2%) had moderate to profound GDD/ID. The common coexisting conditions were epilepsy (68 [63%]), autism spectrum disorder (ASD, 6 [5.5%]), facial dysmorphism (15 [14%]), microcephaly (14 [13.1%]), macrocephaly (8 [7.5%]), hearing loss (7 [6.7%]), and vision impairment (14 [13.5%]). Fifteen of 64 (25%) patients had low weight, and 5/61 (8.2%) had short stature. Compared with ARID and XLID, patients with ADID had an increased rate of ASD (6 [15.4%] vs 0 vs 0) and a decreased rate of brain MRI abnormalities (21[53.8%] vs 40[81.6%] vs 11[73.3%]) (Table 2).
Table 2
| Total | AR | AD | XL | p value |
(N = 108) | % | (N = 50) | % | (N = 40) | % | (N = 18) | % |
Severity of GDD/ID | | | | | | | | | 0.109 |
mild | 7/90 | 7.8 | 1/45 | 2.2 | 4/31 | 12.9 | 2/14 | 14.3 | |
moderate | 10/90 | 11.1 | 4/45 | 8.9 | 3/31 | 9.7 | 3/14 | 21.4 | |
severe | 67/90 | 74.4 | 40/45 | 86.7 | 21/31 | 67.7 | 7/14 | 50.0 | |
profound | 6/90 | 6.7 | 1/45 | 2.2 | 3/31 | 9.7 | 2/14 | 14.3 | |
Epilepsy | 68/108 | 63 | 29/50 | 58 | 28/40 | 70 | 11/18 | 61.1 | 0.496 |
Autism spectrum disorder | 6/110 | 5.5 | 0/50 | 0 | 6/39 | 15.4 | 0/18 | 0 | 0.003 |
EEG abnormality | 70/108 | 64.8 | 29/50 | 58 | 29/40 | 73.8 | 12/18 | 66.7 | 0.353 |
Abnormal Brain MRI | 72/103 | 69.9 | 40/49 | 81.6 | 21/39 | 53.8 | 11/15 | 73.3 | 0.018 |
Facial dysmorphism | 15/107 | 14 | 4/49 | 8.2 | 7/40 | 17.5 | 4/18 | 22.2 | 0.221 |
Visual impairment | 14/104 | 13.5 | 11/48 | 22.9 | 2/39 | 5.1 | 1/17 | 5.9 | 0.038 |
Hearing loss | 7/105 | 6.7 | 6/49 | 12.2 | 1/39 | 2.6 | 0/17 | 0 | 0.140 |
Head circumference anomaly | 22/107 | 20.6 | 13/50 | 26.0 | 4/36 | 10.0 | 5/18 | 27.8 | 0.160 |
microcephaly | 14/107 | 13.1 | 10/50 | 20.0 | 1/36 | 2.5 | 4/18 | 22.2 | |
macrocephaly | 8/107 | 7.5 | 3/50 | 6.0 | 3/36 | 7.5 | 1/18 | 5.6 | |
Weight | | | | | | | | | 0.225 |
Overweight | 1/64 | 1.5 | 0/28 | 0 | 0/27 | 0 | 1/9 | 11.1 | |
Low weight | 16/64 | 25 | 9/28 | 32.1 | 5/27 | 12.5 | 2/9 | 22.2 | |
Short stature | 5/61 | 8.2 | 3/25 | 12 | 1/26 | 3.8 | 1/10 | 10 | 0.372 |
Organ involvement | | | | | | | | | - |
heart | 4/107 | 3.7 | 4/51 | 7.8 | 0/40 | 0 | 0/17 | 0 | 0.160 |
liver | 8/107 | 7.5 | 7/51 | 13.7 | 1/40 | 2.5 | 0/17 | 0 | 0.078 |
kidney | 1/107 | 0.9 | 1/51 | 2.0 | 0/40 | 0 | 0/17 | 0 | 1 |
hair/skin | 5/108 | 4.6 | 2/51 | 3.9 | 2/40 | 5.0 | 1/18 | 5.6 | 1 |
Positive family history | 9/105 | 8.6 | 5/49 | 10.2 | 2/40 | 5.0 | 2/17 | 11.8 | 0.581 |
Abnormal antenatal tests | 13/106 | 12.3 | 8/50 | 16.0 | 4/40 | 10.0 | 1/17 | 5.9 | 0.556 |
Abnormal birth history | 15/106 | 14.2 | 5/50 | 10.0 | 8/40 | 20.0 | 2/17 | 11.8 | 0.442 |
AR, autosomal recessive; AD, autosomal dominant; XL, X-linked; GDD, global developmental delay; ID, intellectual disability; EEG, electroencephalogram; |
Organ involvement was also observed: 5 (4.5%) patients had heart involvement, 10 (9.1%) had liver involvement, 1 (0.9%) had kidney involvement and 5 (4.5%) had abnormal skin or hair manifestations.
The majority of affected individuals were simplex cases (a single occurrence in a family), and only 9 (8.6%) patients had a positive family history. Notably, 13 (12.3%) individuals had abnormal antenatal findings; among them, 8 patients had abnormal prenatal ultrasound results. In addition, 15 (14.2%) patients had an abnormal birth history. These parameters did not show significant differences among the three groups (Table 2). (The details are listed in Supplement 2.)
3. Variant spectra in 108 monogenic GDD/ID patients
In total, 149 different pathogenic variants were found in 81 different genes among the 108 pedigrees. Of these genes, 42 genes were transmitted in the AR pattern, 26 in the AD pattern and 13 in the XL pattern. In order to analyze the disparity in genetic spectra between different inherited models, repeated variants were included in the calculation. The results are presented in Table 3 and Supplement 3 in detail. Among these disease-causing variants, there were 82 (51.9%) missense variants, 30 (19%) nonsense variants, 29 (18.4%) frameshift variants, 5 (3.2%) small deletion variants, 1 (0.6%) multiexon deletion variant and 11 (7%) variants that caused splicing defects.
Table 3
Analysis of genetic spectra
| Total | AR | AD | XL | P Value |
Number | 158 | 100 | 40 | 18 | |
Origin | | | | | < 0.001 |
paternal | 52 (32.9) | 50 (50.0) | 1 (2.5) | 1 (5.6) | |
maternal | 56 (35.4) | 50 (50.0) | 0 | 6 (33.3) | |
de novo | 50 (31.6) | 0 | 39 (97.5) | 11 (61.1) | |
DNA change | | | | | 0.246 |
substitution | 114 (72.2) | 75 (75.0) | 27 (67.5) | 12 (66.7) | |
deletion | 29 (18.4) | 17 (17.0) | 7 (17.5) | 5 (27.8) | |
duplication | 12 (7.6) | 6 (6.0) | 6 (15.0) | 0 | |
insertion | 3 (1.9) | 2 (2.0) | 0 | 1 (5.6) | |
Amino acid change | | | | | 0.162 |
missense | 82 (51.9) | 55 (55.0) | 18 (45.0) | 9 (50.0) | |
nonsense | 30 (19) | 17 (17.0) | 10 (25) | 3 (16.7) | |
deletion | 5 (3.2) | 2 (2.0) | 1 (2.5) | 2 (11.1) | |
insertion | 0 | 0 | 0 | 0 | |
frameshift | 29 (18.4) | 16 (16.0) | 11 (27.5) | 2 (11.1) | |
splicing defect | 11 (7) | 9 (9.0) | 0 | 2 (11.1) | |
start lost | 1 (0.6) | 1 (1.0) | 0 | 0 | |
Loss of function | 68 (43.0) | 40 (40.0) | 21 (52.5) | 7 (38.9) | 0.383 |
Status | | | | | 0.057 |
novel | 76 (48.1) | 40 (40.0) | 25 (62.5) | 10 (55.6) | |
existing | 82 (51.9) | 60 (60.0) | 15 (37.5) | 8 (44.4) | |
AR, autosomal recessive; AD, autosomal dominant; XL, X-linked; |
Loss of function variants include nonsense, frameshift, start lost, single or multiple exons deletion and canonical ± 1 or 2 splice sites. |
Gene ontology accumulation analyses indicated that those genes took part in multiple biological processes, including nervous system development, nervous impulse transmission, positive regulation of GTPase activity and energy metabolism. Genes associated with ion channel transport and nervous system development were mainly inherited in the AD model, while genes related to metabolism were mainly transmitted in AR or XL patterns (Supplementary Fig. 1).
Among the 81 different causative genes, GLB1 was found in 5 patients; PLA2G6, SCN2A, SHANK3 and STXBP1 in 3 patients each; and ALG1, CDKL5, CHD2, FOXG1, GATAD2B, GFAP, GRIN2B, HEXA, IDS, KCNQ2, PAFAH1B1, PCDH19, PDHA1, SLC9A6 and SYNGAP1 in 2 patients each. The other 61 out of 81 genes were observed to have pathogenic variants only once each in this cohort.
Most variants were unique in this cohort, while two variants were relatively common. One was the c.1343 A > T in the GLB1 gene, which occurred in 5 alleles of 3 patients (patient 42/43/44) among 5 patients with GLB1-related diseases. The other was a de novo variant c.235C > T in GFAP, which was detected in two unrelated patients (Nos. 36 and 37) with Alexander Disease. It was a variant that had been reported several times[34–36] but absent in the Normal Population Database (GnomAD and 1000G). Additionally, two homozygous substitution variants, c.1510C > A and c.1510C > T, were found in two patients (Nos. 50 and 51) with Tay-Sachs disease. Multiple studies[37–39] have reported the pathogenicity of these variants, suggesting that the 1510th base pair in the coding sequence of HEXA (NM_000520) was a common variant position.
Notably, 76 (46.9%) variants were identified as novel variants, and 86 (53.1%) variants have been included in disease databases (ClinVar or HGMD) or reported in PubMed articles. The rate was similar to that in previous studies[40–44]. The proportions of novel variants in ARID, ADID and XLID were 40%, 62% and 50%, respectively. This suggests that variant spectra in known ID genes have not been fully explored in all inheritance patterns. The higher rate of novel variants in ADID might be explained by the fact that most variants arose de novo in the AD pattern.
The major difference among ARID, ADID and XLID lies in the origin of variants. Of the 50 patients with ARID, 44 (88%) patients carried compound heterozygous variants, and 6 (12%) patients harbored homozygous variants. We confirmed that in all patients, the two abnormal alleles were separately inherited from healthy outbred parents who carried the heterozygous variants. Among 40 patients with ADID, 39 (97.5%) variants arose de novo. Of the 18 patients with XLID, 11 (61.1%) patients (2 male, 9 female) had de novo variants, 5 male patients harbored hemizygous variants inherited from their asymptomatic heterozygous mother, and 1 female (patient 70) inherited the heterozygous variant c.445C > T in PCDH19 from her non-symptomatic father. This unique characteristic was supported by previous reports [45].
In addition, parental somatic mosaicism was found in 2 cases. Patient 33, who presented with facial dysmorphism and GDD, had a c.941del in GATAD2B. The variant was also detected at a low frequency in his paternal peripheral blood genomic DNA but absent in samples of his healthy mother and sister. Therefore, it is likely that the father carries somatic and germline mosaicism for this variant. In addition, patient 93 harbored a hemizygous c.1153C > T in SLC9A6, and his mother was suspected to have the variant in mosaic state with a low peak in her peripheral blood Sanger sequencing.
4. Prenatal diagnosis results
In total, 43 families underwent prenatal tests to determine whether the next child would harbor the same pathogenic variants as the proband in the fetal period. As demonstrated in Table 4 and Supplement 4, among them, 24 cases were ARID, 13 cases were ADID and 6 were XLID. Thirty-six (83.7%) patients chose amniocentesis, and 7 (16.3%) patients underwent chorionic villus sampling. Among the 24 AR cases, 6 fetuses were found to carry two pathogenic variants that originated from parents who were healthy carriers, 13 fetuses harbored one variant, and 5 fetuses did not have any variants. Among the 14 AD cases, 12 fetuses did not have the variants, while 2 fetuses carried the same variants as the proband in the GATAD2B gene. Of the 6 XL cases, only 1 fetus harbored the pathogenic variant. All variants carried by fetuses were verified after birth or induction of labor.
Table 4
Results of prenatal diagnosis
| Total | AR | AD | XL | P Value |
Number of patients | 43 | 24 | 13 | 6 | |
Pregnancy status at counseling | | | | | 0.629 |
not pregnant | 26 (56.5) | 14 (58.3) | 7 (53.8) | 2 (33.3) | |
pregnant | 20 (43.5) | 10 (41.7) | 6 (46.2) | 4 (66.7) | |
Sample | | | | | 0.738 |
Amniotic fluid | 36 (83.7) | 19 (79.2) | 12 (92.3) | 5 (83.3) | |
Chorionic villus | 7 (16.3) | 5 (20.8) | 1 (7.7) | 1 (16.7) | |
Number of variants carried by the fetus | | | | | 0.001 |
2 | 6 (14.0) | 6 (25.0) | - | - | |
1 | 16 (37.2) | 13 (54.2) | 2 (15.4) | 1 (16.7) | |
0 | 21 (48.8) | 5 (20.8) | 11 (84.6) | 5 (833) | |
AR, autosomal recessive; AD, autosomal dominant; XL, X-linked; |
The appropriate time for genetic counseling is before the next pregnancy, owing to the additional procedure to confirm original molecular tests. In this study, 20 (46.5%) families had been pregnant before referral to genetic counseling and prenatal diagnosis, which might influence further management. It has been suggested that, for most families in China in which a proband with a rare monogenic GDD/ID, referral to genetic counseling is usually delayed and reflects a shortage of related resources. Therefore, timely genetic counseling after index patients obtain a genetic diagnosis, should be emphasized to families who plan to have additional children.