Molecular profiles and long-term outcomes of Thai children with hepatic glycogen storage disease in Thailand

Table 1 Genetic variants associated with glycogen storage disease

Patient number	Gene	WES	Variant	Amino acid	Exon/Intron	Zygosity	Inheriting parent of allele1	Transcript	hg19 coordinate	Ref.
GSD Ia
5	G6PC	Duo	c.648G>T	p.Leu216Leu	Exon 5	Homozygous or Hemizygous2	Mother	NM_000151.4	chr17:41063017 G>T	[21]
GSD III
3	AGL	Trio	c.2578delG	p.Val860LeufsTer8	Exon 20	Homozygous	Father and mother	NM_000642.3	chr1:100350156 delG	Clinvar RCV003060970.13
4	AGL	Singleton	c.1611+1G>C	N/A	Intron 12	Heterozygous	Unknown	NM_000642.3	chr1:100343385 G>C	Novel4
			c.1735G>A	p.Glu579Lys	Exon 13	Heterozygous	Unknown	NM_000642.3	chr1:100345602 G>A	Novel4
6	AGL	Trio	c.1735+1G>T	N/A	Intron 13	Homozygous	Father and mother	NM_000642.3	chr1:100345603 G>T	[22]
GSD VI
2	PYGL	Trio	c.514C>T	p.Arg172Ter	Exon 4	Heterozygous	Father	NM_002863.5	chr14:51398405 G>A	[9]
			c.2467C>T	p.Gln823Ter	Exon 20	Heterozygous	Mother	NM_002863.5	chr14:51372187 G>A	[9]
7	PYGL	Singleton	c.2467C>T	p.Gln823Ter	Exon 20	Heterozygous	Unknown	NM_002863.5	chr14:51372187 G>A	[9]
			c.932G>A	p.Arg311His	Exon 8	Heterozygous	Unknown	NM_002863.5	chr14:51383747 C>T	[23]
8	PYGL	Trio	c.1726C>T	p.Arg576Ter	Exon 14	Heterozygous	Father	NM_002863.5	chr14:51378916 G>A	[24]5
			c.2467C>T	p.Gln823Ter	Exon 20	Heterozygous	Mother	NM_002863.5	chr14:51372187 G>A	[9]
GSD IX
1	PHKA2	Trio	c.2746C>T	p.Arg916Trp	Exon 25	hemizygous	Mother	NM_000292.3	chrX:18924673 G>A	[25]

¹Biallelic variants identified by singleton exome sequencing analysis will be reported as "parental origin unknown.

²The duo exome sequencing performed on patient #5 and the mother, due to the unavailability of the father's DNA, has shown that the zygosity of the G6PC:c.648G>T variant cannot be distinguished between homozygous (inherited from both parents) and hemizygous (inherited from the mother only).

³Although no individuals with AGL-related conditions have been previously reported in the literature with this variant, ClinVar classifies the AGL:c.2578delG variant as pathogenic (Accession: RCV003060970.1) based on a submission ID: SCV003456543.1 by Invitae.

⁴Novel: a novel variant means that it is not present in the public database including literatures in pubmed, GRCh38/hg38 or GRCh37/hg19 gnomAD, and Clinvar databases.

⁵No reports of the PYGL:c.932G>A (p.Arg311His) variant exist in patients with glycogen storage disease type VI. However, the literature on colorectal carcinoma documents its presence[24].

WES: Whole-exome sequencing; GSD: Glycogen storage diseases.

Table 2 Comparison of novel AGL variants based on allele frequency and functional impact

Variant	GRCh37/hg19 gnomAD	GRCh38/hg38 gnomAD	5432 Thai exomes	Potential functional impact	Reported in other GSD cases	ACMG classification
c.1611+1G>C (p.?)	Not identified	Not identified	Not identified	Potentially disruptive to splicing due to its location at the splice donor site. May lead to aberrant mRNA processing and protein expression	Not reported	Likely pathogenic (PVS1, PM2)
c.1735G>A (p.Glu579Lys)	Not identified	Identified in 1 out of 1461034 alleles	Not identified	Missense mutation resulting in a Glu579Lys amino acid change within the transferase catalytic domain. May affect enzyme activity or protein stability	Not reported	Variant of uncertain significance (PM2, PP3)

ACMG: American College of Medical Genetics and Genomics; GSD: Glycogen storage diseases.

Table 3 Patient characteristics, biological profiles at the time of clinical diagnosis and at the last of follow-up

Patient number	Sex	Age at clinical Dx (year)	Time from clinical Dx to molecular Dx (year)	First presentation	Growth and nutritional status	Biochemical result						Follow-up time (year)	Clinical and biological profiles at the last follow-up
						AST (U/L)	ALT (U/L)	BS (mg/dL)	TC (mg/dL)	TG (mg/dL)	Uric Acid (mg/dL)		Growth and nutritional status	AST (U/L)	ALT(U/L)	BS (mg/dL)	TC (mg/dL)	TG (mg/dL)	Uric Acid (mg/dL)
GSD I
5	F	14.7	12.52	Hepatomegaly, recurrent epistaxis	Wasting/ stunting	118	67	53	210	376	8.6	13.8	Stunting	33	28	58	179	396	9.7
GSD III
3	F	3.02	8.49	Hepatomegaly	Normal	4302	1341	48	241	622	5.1	11.5	Overweight	510	375	72	205	124	8
4	F	1.43	12.22	Hepatomegaly	Normal	629	547	20	138	119	3.3	12.3	Normal	33	28	78	137	63	5.8
6	M	2.62	3.06	Hepatomegaly, doll-like facies	Stunting	1878	854	30	180	231	6.1	3.1	Normal	626	408	35	184	203	6.8
GSD VI
2	F	1.75	9.24	Hepatomegaly	Wasting	746	736	56	305	335	6.9	12.5	Normal	15	14	83	137	89	6.1
7	F	3.08	2.08	Hepatomegaly	Stunting	72	64	92	256	189	4.3	2.1	Normal	55	40	72	226	104	5.9
8	M	1.35	1.10	Hepatomegaly, doll-like facies	Overweight/ stunting	920	665	55	246	303	3.9	1.8	Overweight	72	90	86	170	100	5.4
GSD IX
1	M	1.7	2.75	Hepatomegaly, doll-like facies	Stunting	1531	439	34	145	159	5.3	6.48	Overweight/stunting	161	78	84	145	97	5.2

GSD: Glycogen storage disease; F: Female; M: Male, Dx: Diagnosis; AST: Aspartate aminotransferase; ALT: Alanine aminotransferase; BS: Blood sugar; TC: Total cholesterol; TG: Triglyceride.

Table 4 Biochemical profiles at the diagnosis and the last follow-up, median (25^th-75^th percentiles)

Blood test	At the diagnosis	At the last follow-up	P value
Hb (mg/dL)	11.9 (10.1-12.2)	12.9 (11.8-13.1)	0.072
WBC	11140 (9975-14020)	9415 (8600-10690)	0.046
Platelet	386000 (325500-457500)	377500 (327000-448000)	1
Blood sugar (mg/dL)	55 (30-87)	72 (58-83.5)	0.248
Total cholesterol	241 (138-256)	174.5 (137-194.5)	0.132
Triglyceride (mg/dL)	231 (159-335)	105.5 (94.5-163.5)	0.037
LDL (mg/dL)	141 (88-211)	94 (83.5-122)	0.165
HDL (mg/dL)	24 (10-32)	39.5 (35-41)	0.004
Uric acid (mg/dL)	5.1 (3.9-6.5)	6 (5.6-7.55)	0.148
ALT (U/L)	665 (67-854)	59 (28-232.5)	0.021
AST (U/L)	833 (374-1704)	63.5 (33-335.5)	0.007
Total bilirubin (mg/dL)	0.39 (0.24-0.99)	0.53 (0.43-0.70)	0.462
Direct bilirubin (mg/dL)	0.22 (0.10-0.41)	0.22 (0.16-0.28)	1
Globulin (mg/dL)	3.1 (2.8-3.4)	3.4 (2.85-4.05)	0.354
Albumin (mg/dL)	4.3 (4.0-4.5)	4.4 (4.25-4.4)	0.335
GGT	169 (66.2-251)	59 (31.5-136)	0.156
Blood urea nitrogen	12 (8-14)	10.5 (9.5-13.5)	0.771
Creatinine	0.25 (0.21-0.4)	0.41 (0.26-0.55)	0.072

Hb: Hemoglobin; WBC: White blood cell count; LDL: Low density lipoprotein; HDL: High density lipoprotein; ALT: Alanine aminotransferase; AST: Aspartate aminotransferase; GGT: Gamma-glutamyl transferase.