NM_000512.5(GALNS):c.1429_1455del (p.Glu477_Gln485del) AND Mucopolysaccharidosis, MPS-IV-A

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Feb 1, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001261588.4

Allele description [Variation Report for NM_000512.5(GALNS):c.1429_1455del (p.Glu477_Gln485del)]

NM_000512.5(GALNS):c.1429_1455del (p.Glu477_Gln485del)

Genes:

LOC126862447:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:88884193-88885392 [Gene]
GALNS:galactosamine (N-acetyl)-6-sulfatase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_000512.5(GALNS):c.1429_1455del (p.Glu477_Gln485del)

HGVS:

NC_000016.10:g.88818038_88818064del
NG_008667.1:g.43907_43933del
NM_000512.5:c.1429_1455delMANE SELECT
NM_001323543.2:c.874_900del
NM_001323544.2:c.1447_1473del
NP_000503.1:p.Glu477_Gln485del
NP_001310472.1:p.Glu292_Gln300del
NP_001310473.1:p.Glu483_Gln491del
NC_000016.9:g.88884446_88884472del

Links:

dbSNP: rs1909818289

NCBI 1000 Genomes Browser:

rs1909818289

Molecular consequence:

NM_000512.5:c.1429_1455del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001323543.2:c.874_900del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001323544.2:c.1447_1473del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Mucopolysaccharidosis, MPS-IV-A (MPS4A)
Synonyms:: MPS IVA; Morquio syndrome A; MPS 4A; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009659; MedGen: C0086651; Orphanet: 309297; Orphanet: 582; OMIM: 253000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001438857	Pathology and Clinical Laboratory Medicine, King Fahad Medical City	no assertion criteria provided (ACMG Guidelines, 2015)	Pathogenic	germline	clinical testing	Citation Link,
SCV001547966	Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 1, 2021)	germline	curation	PubMed (3) [See all records that cite these PMIDs] 24726177, 34387910, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001438857

Pathology and Clinical Laboratory Medicine, King Fahad Medical City

no assertion criteria provided

(ACMG Guidelines, 2015)

Pathogenic

germline

clinical testing

Citation Link,

SCV001547966

Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 1, 2021)

germline

curation

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	curation
Arab	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Molecular testing of 163 patients with Morquio A (Mucopolysaccharidosis IVA) identifies 39 novel GALNS mutations.

Morrone A, Tylee KL, Al-Sayed M, Brusius-Facchin AC, Caciotti A, Church HJ, Coll MJ, Davidson K, Fietz MJ, Gort L, Hegde M, Kubaski F, Lacerda L, Laranjeira F, Leistner-Segal S, Mooney S, Pajares S, Pollard L, Ribeiro I, Wang RY, Miller N.

Mol Genet Metab. 2014 Jun;112(2):160-70. doi: 10.1016/j.ymgme.2014.03.004. Epub 2014 Mar 20. Erratum in: Mol Genet Metab. 2014 Nov;113(3):237.

PubMed [citation]

PMID:: 24726177
PMCID:: PMC4203673

Molecular basis of mucopolysaccharidosis IVA (Morquio A syndrome): A review and classification of GALNS gene variants and reporting of 68 novel variants.

Zanetti A, D'Avanzo F, AlSayed M, Brusius-Facchin AC, Chien YH, Giugliani R, Izzo E, Kasper DC, Lin HY, Lin SP, Pollard L, Singh A, Tonin R, Wood T, Morrone A, Tomanin R.

Hum Mutat. 2021 Nov;42(11):1384-1398. doi: 10.1002/humu.24270. Epub 2021 Aug 23. Review.

PubMed [citation]

PMID:: 34387910
PMCID:: PMC9291100

See all PubMed Citations (3)

Details of each submission

From Pathology and Clinical Laboratory Medicine, King Fahad Medical City, SCV001438857.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Arab	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, SCV001547966.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (3)

Description

Absent from gnomAD v2.1.1 (PM2_moderate); protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants (PM4_moderate)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 26, 2023

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