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NM_000262.3(NAGA):c.479C>G (p.Ser160Cys) AND Alpha-N-acetylgalactosaminidase deficiency type 3

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 1, 1996
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000019795.27

Allele description [Variation Report for NM_000262.3(NAGA):c.479C>G (p.Ser160Cys)]

NM_000262.3(NAGA):c.479C>G (p.Ser160Cys)

Genes:
LOC126863160:CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:42462918-42464117 [Gene]
NAGA:alpha-N-acetylgalactosaminidase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.2
Genomic location:
Preferred name:
NM_000262.3(NAGA):c.479C>G (p.Ser160Cys)
HGVS:
  • NC_000022.11:g.42067136G>C
  • NG_009247.1:g.8707C>G
  • NM_000262.3:c.479C>GMANE SELECT
  • NM_001362848.1:c.479C>G
  • NM_001362850.1:c.479C>G
  • NP_000253.1:p.Ser160Cys
  • NP_001349777.1:p.Ser160Cys
  • NP_001349779.1:p.Ser160Cys
  • NC_000022.10:g.42463140G>C
  • NM_000262.2:c.479C>G
  • P17050:p.Ser160Cys
Protein change:
S160C; SER160CYS
Links:
UniProtKB: P17050#VAR_000496; OMIM: 104170.0004; dbSNP: rs121434532
NCBI 1000 Genomes Browser:
rs121434532
Molecular consequence:
  • NM_000262.3:c.479C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362848.1:c.479C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362850.1:c.479C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Alpha-N-acetylgalactosaminidase deficiency type 3
Synonyms:
SCHINDLER DISEASE, TYPE III; Schindler disease, type 3; ALPHA-N-ACETYLGALACTOSAMINIDASE DEFICIENCY, TYPE III
Identifiers:
MONDO: MONDO:0019264; MedGen: C5437471

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000040093OMIM
no assertion criteria provided
Pathogenic
(Jun 1, 1996) 		germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

alpha-N-acetylgalactosaminidase deficiency with mild clinical manifestations and difficult biochemical diagnosis.

de Jong J, van den Berg C, Wijburg H, Willemsen R, van Diggelen O, Schindler D, Hoevenaars F, Wevers R.

J Pediatr. 1994 Sep;125(3):385-91.

PubMed [citation]
PMID:
8071745

Human alpha-N-acetylgalactosaminidase (alpha-NAGA) deficiency: new mutations and the paradox between genotype and phenotype.

Keulemans JL, Reuser AJ, Kroos MA, Willemsen R, Hermans MM, van den Ouweland AM, de Jong JG, Wevers RA, Renier WO, Schindler D, Coll MJ, Chabas A, Sakuraba H, Suzuki Y, van Diggelen OP.

J Med Genet. 1996 Jun;33(6):458-64.

PubMed [citation]
PMID:
8782044
PMCID:
PMC1050630
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000040093.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In a Dutch girl with type III NAGA deficiency (609241) reported by de Jong et al. (1994), Keulemans et al. (1996) identified compound heterozygosity for 2 mutations in the NAGA gene: E325K (104170.0001) and a 4969C-G transversion in exon 4 (numbering according to Yamauchi et al., 1990), resulting in a ser160-to-cys (S160C) substitution. The same genotype was found in the clinically unaffected 3-year-old brother of the proband, and the authors suggested that the brother might be a preclinical case of NAGA deficiency; the brother's twin sister did not have the genotype. Residual enzyme activity in the proband was approximately 4% of controls. The S160C allele was not identified in 80 Dutch control alleles.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 28, 2024