Alternative titles; symbols
HGNC Approved Gene Symbol: ALG13
SNOMEDCT: 733451007;
Cytogenetic location: Xq23 Genomic coordinates (GRCh38): X:111,681,170-111,760,649 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| Xq23 | Developmental and epileptic encephalopathy 36 | 300884 | X-linked | 3 |
Asparagine (N)-glycosylation is an essential modification that regulates protein folding and stability. ALG13 and ALG14 (612866) constitute the UDP-GlcNAc transferase, which catalyzes a key step in endoplasmic reticulum N-linked glycosylation (summary by Averbeck et al., 2007).
By database analysis, followed by PCR of human whole brain cDNA, Gao et al. (2005) cloned ALG13. The deduced 161-amino acid protein has a calculated molecular mass of 18.2 kD and shares 28% sequence identity with yeast Alg13. Alg13 contains a predicted catalytic domain but lacks a membrane-spanning domain. Fluorescence microscopy and subcellular fractionation studies localized the S. cerevisiae Alg13 protein to the endoplasmic reticulum membrane.
There are multiple isoforms of the ALG13 gene. Using RT-PCR, Esposito et al. (2013) found expression of 3 isoforms in human ovary, kidney, pancreas, brain, testis, lung, and heart. The short isoforms 2 and 3 also showed high expression in liver and low expression in muscle. Mouse Alg13 was expressed in the mouse podocyte.
Gao et al. (2005) used coimmunoprecipitation studies to demonstrate interaction between S. cerevisiae Alg13 and Alg14 proteins. By individual and joint overexpression of Alg13 and Alg14, followed by cell localization studies, they showed that localization of Alg13 to the ER membrane is dependent upon its association with Alg14, and that increasing Alg14 levels to match those of Alg13 restored Alg13 localization to the ER. Gao et al. (2005) concluded that Alg13 recruitment to the ER is mediated by Alg14. Human ALG13 and ALG14 each functionally complemented the corresponding Alg13 and Alg14 mutants in S. cerevisiae to partially restore the defective glycosylation phenotype. Gao et al. (2005) suggested that the human ALG13 and ALG14 proteins interact with each other to form a functional UDP-GlcNAc transferase.
Using functional analysis of S. cerevisiae Alg13/Alg14 chimeras and in vitro protease protection assays, Averbeck et al. (2007) concluded that Alg13 and Alg14 comprise a novel bipartite UDP-GlcNAc glycosyltransferase that catalyzes the second sugar addition in the synthesis of the dolichol-linked oligosaccharide precursor in N-linked glycosylation. Alg14 is a membrane protein that recruits the soluble Alg13 catalytic subunit from the cytosol to the face of the ER membrane where the reaction occurs.
Stumpf (2020) mapped the ALG13 gene to chromosome Xq23 based on an alignment of the ALG13 sequence (GenBank BC117379) with the genomic sequence (GRCh38).
Developmental and Epileptic Encephalopathy 36
In a 10-year-old girl (trio 37) with developmental and epileptic encephalopathy-36 (DEE36; 300884), de Ligt et al. (2012) identified a de novo heterozygous missense mutation in the ALG13 gene (N107S; 300776.0002). The patient was ascertained from a larger cohort of 100 patients with severe intellectual disability who underwent exome sequencing. The patient also carried a de novo heterozygous E89K variant in the KRT32 gene (602760) that was not thought to be pathogenic. The Epi4K Consortium and Epilepsy Phenome/Genome Project (2013) identified a de novo heterozygous N107S mutation in 2 unrelated girls with DEE36. The patients were part of a larger cohort of 264 probands with epileptic encephalopathy who underwent exome sequencing. Isoelectric focusing of serum transferrin was not reported in the girls with the N107S mutation. Functional studies of the variant were not performed.
In a Caucasian boy with DEE36 who died at age 1 year, Timal et al. (2012) identified a hemizygous missense mutation in the ALG13 gene (K94E; 300776.0001). The mutation was identified by exome sequencing and confirmed by Sanger sequencing. Studies of patient-derived cells showed decreased enzyme activity, at about 17% of wildtype. The patient was 1 of 6 patients with unsolved CDG type I from unrelated families who underwent whole-exome sequencing.
Michaud et al. (2014) identified a de novo heterozygous N107S mutation in the ALG13 gene in a girl with DEE36. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing. Functional studies of the variant were not performed. The girl also had a heterozygous 9p24.2 deletion inherited from her unaffected mother that was predicted to be benign. Michaud et al. (2014) postulated that ALG13 mutations in girls may represent either a dominant-negative or a gain-of-function effect.
Dimassi et al. (2016) identified a de novo heterozygous N107S mutation in a 6-year-old girl with DEE36. Functional studies of the variant were not performed.
In a female infant with DEE36, Bastaki et al. (2018) identified heterozygosity for the N107S mutation in the ALG13 gene.
Ng et al. (2020) reported 29 individuals with de novo heterozygous or hemizygous mutations in the ALG13 gene who were identified through next-generation sequencing. Two recurrent mutations accounted for the majority: N107S, found in 23 of 29 (79%) patients, and A81T (300776.0004), found in 3 (10%) individuals. Clinical details, available for 26 patients, were consistent with DEE36 and a diagnosis of early-onset seizures with West syndrome. There were only 2 males in the cohort. One (CDG-0083) had a hemizygous N107S mutation and a phenotype consistent with DEE36. The other (CDG-0101) had a de novo G972V mutation that was not present in the gnomAD database; clinical details were limited and he was noted to be mosaic for the mutation. All 14 patients tested had normal transferrin glycosylation. Two patients had mildly abnormal glycosylation studies consistent with a type I defect, but both had resolution of these biochemical abnormalities, which were later in the normal range. In vitro studies in alg13-null yeast showed that both the N107S and A81T variants could restore a growth defect, but were unable to restore abnormal glycosylation of carboxypeptidase Y (CPY). The findings suggested that these mutations affect alg13 function in yeast. Noting that the function of ALG13 in humans remains unclear, Ng et al. (2020) speculated that the heterozygous or hemizygous ALG13 mutations found in patients likely cause a gain-of-function effect with tissue-specific manifestations.
Hamici et al. (2017) identified heterozygosity for the recurrent N107S mutation in the ALG13 gene in a 2-year-old Emirati girl with DEE36. X-chromosome inactivation studies in the patient's leukocytes showed a random pattern of X-chromosome inactivation.
Galama et al. (2018) identified heterozygosity for the N107S mutation in the ALG13 gene in a 3.5-month-old boy with DEE36.
Alsharhan et al. (2021) identified heterozygous mutations in the ALG13 gene in 11 patients (3 males and 8 females) with DEE36. In the 3 male patients, the mutation was inherited from the patient's mother (P100S, 300776.0005; c.2458-15_2486del, 300776.0006; and V758F), although the V758F was considered to be a variant of unknown significance because a patient sample was not available for glycosylation analysis. All of the female patients had de novo mutations, 6 with N107S, 1 with A81T (300776.0004), and 1 with G972V.
In a boy with DEE36, Gadomski et al. (2017) identified hemizygosity for a missense mutation in the ALG13 gene (E463G; 300776.0007). The mutation, which was found by sequencing of a comprehensive expanded epilepsy gene panel, was also identified in heterozygous state in his asymptomatic mother. ICAM1 (147840) protein expression was reduced in patient fibroblasts. Adding galactose to the patient's fibroblasts in vitro increased ICAM1 expression.
Associations Pending Confirmation
See 300776.0003 for discussion of a possible association of focal segmental glomerulosclerosis (FSGS; see 603278) with mutation in the ALG13 gene.
In 4 brothers, born of unrelated Arab parents, with nonsyndromic X-linked mental retardation, Bissar-Tadmouri et al. (2014) identified a hemizygous c.3221A-G transition (NM_001099922.2) in the ALG13 gene, resulting in a tyr1074-to-cys (Y1074C) substitution at a residue conserved in higher vertebrates. The variant, which was found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family; the unaffected mother was heterozygous for the variant. The variant was not found in the dbSNP or 1000 Genomes Project databases or in 65 ethnically matched controls. Functional studies of the variant and studies of patient cells were not performed. Brain imaging was normal and none of the boys had congenital malformations or facial dysmorphisms. N-glycosylation studies could not be performed. Hamosh (2016) noted that on November 29, 2016 the ExAC database listed the Y1074C variant as occurring in 32 hemizygous males of South Asian descent, suggesting that the variant is not pathogenic.
In a Japanese boy with early-onset epileptic encephalopathy, severe intellectual disability, optic atrophy, and septooptic dysplasia, Hino-Fukuyo et al. (2015) identified a hemizygous c.880C-T transition (NM_001099922) in the ALG13 gene, resulting in a pro294-to-ser (P294S) substitution. The mutation, which was found by whole-exome sequencing, was inherited from the unaffected mother. Hamosh (2016) noted that on November 29, 2016 the ExAC database listed the P294S variant as occurring in 3 hemizygous males of East Asian descent, suggesting that the variant is not pathogenic (Hamosh, 2016).
In a Caucasian boy with developmental and epileptic encephalopathy-36 (DEE36; 300884), Timal et al. (2012) identified a hemizygous c.280A-G transition (c.280A-G, NM_001099922.2) in the ALG13 gene, resulting in a lys94-to-glu (K94E) substitution at a highly conserved residue in the C-terminal glycosyltransferase domain. The mutation was identified by exome sequencing and confirmed by Sanger sequencing. The mutation was not present in the blood of the mother, but was present on the maternally inherited allele, suggesting either maternal germline mosaicism or a de novo event. The patient had refractory epilepsy, hepatomegaly, recurrent infections, increased bleeding tendency, microcephaly, horizontal nystagmus, bilateral optic nerve atrophy, and extrapyramidal and pyramidal signs. He died at age 1 year. Transferrin isoelectric focusing showed abnormal N-glycosylation and was consistent with a diagnostic classification of a congenital disorder of glycosylation. Studies of patient-derived cells showed decreased enzyme activity, at about 17% of wildtype.
In a 10-year-old girl with developmental and epileptic encephalopathy-36 (DEE36; 300884), de Ligt et al. (2012) identified a de novo heterozygous c.320A-G transition in the ALG13 gene, resulting in an asn107-to-ser (N107S) substitution. The patient was ascertained from a larger cohort of 100 patients with severe intellectual disability who underwent exome sequencing. The patient also carried a de novo heterozygous E89K variant in the KRT32 gene (602760) that was not thought to be pathogenic. The patient was born at 34 weeks' gestation and showed neonatal feeding problems, hypotonia, seizures, and severely delayed psychomotor development. She had a large head circumference (greater than 2.5 SD), and brain MRI showed hydrocephalus, myelination delay, and wide sulci. Other features included self-mutilation, sleep disturbance, and dysmorphic features, such as hypertelorism, broad coarse face, low-set ears, mild retromicrognathia, small hands and feet, joint contractures, and scoliosis. Isoelectric focusing of serum transferrin was not performed.
The Epi4K Consortium and Epilepsy Phenome/Genome Project (2013) identified a de novo heterozygous N107S mutation in 2 unrelated girls (trios ij and dg) with early-onset epileptic encephalopathy. The patients were part of a larger cohort of 264 probands with epileptic encephalopathy who underwent exome sequencing. The patients had onset of seizures at ages 1 and 4 months, respectively. EEG showed hypsarrhythmia. Both showed severely delayed psychomotor development after the onset of seizures. A statistical likelihood analysis indicated that the probability of this finding occurring by chance was p = 7.8 x 10(-12). Functional studies were not performed.
Michaud et al. (2014) identified a de novo heterozygous N107S mutation (c.320A-G, NM_001099922.2) in the ALG13 gene in a girl with DEE36. The mutation was found by whole-exome sequencing. Functional studies of the variant were not performed. The girl also had a heterozygous 9p24.2 deletion inherited from her unaffected mother that was predicted to be benign.
Smith-Packard et al. (2015) reported a 7-year-old girl with DEE36 who carried a de novo heterozygous N107S mutation identified by whole-genome sequencing. The patient had normal glycosylation of serum transferrin. Functional studies of the variant and studies of patient cells were not performed; however, the authors noted that the mutation occurs at a highly conserved residue within a loop deep inside the protein in a presumed functional domain, and thus may impact the catalytic activity. She presented at 8 months of age with infantile spasms associated with hypsarrhythmia on EEG. She had severe cognitive impairment with limited speech.
Dimassi et al. (2016) identified a de novo heterozygous N107S mutation in a 6-year-old girl with DEE36. The mutation was found by whole-exome sequencing of 10 parent-child trios. The patient had normal glycosylation of serum transferrin. The mutation was not reported in the ExAC database; functional studies of the variant were not performed. At 2 months of age, the patient developed infantile spasms associated with hypsarrhythmia on EEG and thereafter showed severely delayed psychomotor development with inability to sit and limited eye contact.
Ng et al. (2020) identified a de novo heterozygous N107S mutation in the ALG13 gene in 23 patients who underwent next-generation sequencing. Clinical details were consistent with DEE36 and a diagnosis of early-onset seizures with West syndrome. All but 1 were female: the 1 male patient with the mutation (CDG-0083) had a phenotype consistent with DEE36. Ng et al. (2020) noted that the N107S variant is not present in the gnomAD database. In vitro studies in alg13-null yeast showed that the N107S variant could restore a growth defect, but was unable to restore abnormal glycosylation of carboxypeptidase Y (CPY). The findings suggested that these mutations affect alg13 function in yeast. None of the patients tested showed evidence of a glycosylation defect, although 1 patient (CDG-1017) had mild and transient abnormalities that later resolved to normal. The patients had onset of infantile spasms at a mean age of 6.5 months; most had hypsarrhythmia on EEG, consistent with West syndrome. All had global developmental delay with impaired intellectual development.
In a 2-year-old Emirati girl with DEE36, Hamici et al. (2017) identified heterozygosity for the N107S mutation in the ALG13 gene. The de novo mutation was identified by whole-exome sequencing and confirmed by Sanger sequencing. X-chromosome inactivation studies in the patient's leukocytes showed a random pattern of X-chromosome inactivation. The patient had severe infantile epileptic encephalopathy.
In a 3.5-month-old boy with DEE36, Galama et al. (2018) identified heterozygosity for the N107S mutation in the ALG13 gene. The de novo mutation was identified by whole-exome sequencing. This patient was the first male with DEE36 to be identified with the N107S mutation in the ALG13 gene.
This variant is classified as a variant of unknown significance because its contribution to focal segmental glomerulosclerosis (FSGS; see 603278) has not been confirmed.
Esposito et al. (2013) reported a large 6-generation Australian family in which 12 males had focal segmental glomerulosclerosis resulting in progressive renal failure. The pattern was consistent with X-linked recessive inheritance, although some carrier females had proteinuria or preeclampsia. Six of the males with FSGS also had a progressive cardiac conduction disorder, necessitating a pacemaker in 5 patients. Linkage analysis for FSGS identified a 21.19-cM candidate disease interval on chromosome Xq21.33-q24 between DXS8077 and DXS8064 (lod score of 3.32 at DXS1106). Whole-exome sequencing of 2 affected males identified 2 variants in 2 different genes: an R113W substitution in the NXF5 gene (300319.0001), and an AC-TT change at nucleotides 421 and 422 in exon 6 of the ALG13 gene. The variants were not found in the 1000 Genomes Project database, in 6 in-house control exomes, or in 598 control chromosomes, and Sanger sequencing showed that both variants segregated with the disorder in the family. Both variants were on the same haplotype. The mutant ALG13 mRNA was detected in cells from both male and female mutation carriers. The AC-TT change in the ALG13 gene change occurs in an intronic region in the long isoform 1 and causes a thr141-to-leu (T141L) substitution in exon 6 of isoform 2 and an asn121-to-ile (N121I) substitution in exon 6 of isoform 3. In vitro functional expression studies showed no difference in expression or subcellular localization for the T141L mutant protein, suggesting that the variant may not have a pathogenic effect. However, Esposito et al. (2013) could not rule out a small effect of T141L or N121I on the disease phenotype.
In 3 unrelated female patients (CDG-0085, CDG-0089, and CDG-0417) with developmental and epileptic encephalopathy-36 (DEE36; 300884), Ng et al. (2020) identified a de novo heterozygous c.241G-A transition in the ALG13 gene, resulting in an ala81-to-thr (A81T) substitution at a conserved residue close to the UDP-GlcNAc substrate-binding site. The mutation, which was found by next-generation sequencing, was not present in the gnomAD database. Western blot analysis of patient fibroblasts showed normal levels of the mutant protein. In vitro studies in alg13-null yeast showed that the A81T variant could restore the growth defect, but was unable to restore abnormal glycosylation of CPY. The findings suggested that the mutation affected alg13 function in yeast. Two patients had onset of infantile spasms at 1 month of age, and the third had onset at 9 months of age. Patient CDG-0417 had transient evidence of a mild type I glycosylation defect, but this later resolved and showed normal results.
In a female patient with DEE36, Alsharhan et al. (2021) identified a de novo heterozygous A81T mutation in the ALG13 gene.
In a 6-year-old Afro-Caribbean male (patient 1) with developmental and epileptic encephalopathy-36 (DEE36; 300884), Alsharhan et al. (2021) identified a heterozygous c.3013C-T transition in the ALG13 gene, resulting in a pro100-to-ser (P100S) substitution. The mutation was also identified in the mother. The mutation was not present in the gnomAD database. Semiquantitative plasma N-glycan analysis using ESI-QTOF mass spectrometry demonstrated mild increases in some small high-mannose glycans.
In an 8-year-old Afro-Caribbean male (patient 2) with developmental and epileptic encephalopathy-36 (DEE36; 300884), Alsharhan et al. (2021) identified a heterozygous deletion (c.2458-15_2486del) in the ALG13 gene that was predicted to result in a splicing abnormality. The mutation was also identified in the mother. Carbohydrate-deficient transferrin analysis demonstrated a type I pattern. Semiquantitative plasma N-glycan analysis using ESI-QTOF mass spectrometry demonstrated mild increases in some small high-mannose glycans.
In a boy with developmental and epileptic encephalopathy-36 (DEE36; 300884), Gadomski et al. (2017) identified hemizygosity for a c.1388A-G transition in exon 12 of the ALG13 gene, resulting in a glu463-to-gly (E463G) substitution at a conserved residue. The mutation, which was found by sequencing of a comprehensive expanded epilepsy gene panel, was present in heterozygous state in the unaffected mother. The variant was not reported in 13,100 individuals of European or African American ancestry in the NHLBI Exome Sequencing Project database. ICAM1 (147840) protein expression was reduced in patient fibroblasts, but transferrin isoelectric focusing and mass spectrometry analysis for glycan isoforms were normal in the patient.
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