NC_000016.10:g.(?_88814419)_(88856897_?)del AND Mucopolysaccharidosis, MPS-IV-A

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 28, 2022
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:: RCV000633468.8

Allele description [Variation Report for NC_000016.10:g.(?_88814419)_(88856897_?)del]

NC_000016.10:g.(?_88814419)_(88856897_?)del

Genes:

LOC130059761:ATAC-STARR-seq lymphoblastoid silent region 7882 [Gene]
LOC130059762:ATAC-STARR-seq lymphoblastoid silent region 7883 [Gene]
LOC126862447:CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:88884193-88885392 [Gene]
LOC132090440:Neanderthal introgressed variant-containing enhancer experimental_46374 [Gene]
TRAPPC2L:trafficking protein particle complex subunit 2L [Gene - OMIM - HGNC]
GALNS:galactosamine (N-acetyl)-6-sulfatase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NC_000016.10:g.(?_88814419)_(88856897_?)del

HGVS:

NC_000016.10:g.(?_88814419)_(88856897_?)del
NC_000016.9:g.(?_88880827)_(88923305_?)del

Condition(s)

Name:: Mucopolysaccharidosis, MPS-IV-A (MPS4A)
Synonyms:: MORQUIO SYNDROME A; GALACTOSAMINE-6-SULFATASE DEFICIENCY; GALNS DEFICIENCY; 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
SCV000754697	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 28, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12442278, 8829629, 10479485, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000754697

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 28, 2022)

germline

clinical testing

PubMed (4)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Molecular analysis of Turkish mucopolysaccharidosis IVA (Morquio A) patients: identification of novel mutations in the N-acetylgalactosamine-6-sulfate sulfatase (GALNS) gene.

Terzioglu M, Tokatli A, Coskun T, Emre S.

Hum Mutat. 2002 Dec;20(6):477-8.

PubMed [citation]

PMID:: 12442278

Mucopolysaccharidosis IVA: submicroscopic deletion of 16q24.3 and a novel R386C mutation of N-acetylgalactosamine-6-sulfate sulfatase gene in a classical Morquio disease.

Fukuda S, Tomatsu S, Masuno M, Ogawa T, Yamagishi A, Rezvi GM, Sukegawa K, Shimozawa N, Suzuki Y, Kondo N, Imaizumi K, Kuroki Y, Okabe T, Orii T.

Hum Mutat. 1996;7(2):123-34.

PubMed [citation]

PMID:: 8829629

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000754697.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the GALNS gene has been identified. Loss-of-function variants in GALNS are known to be pathogenic (PMID: 12442278). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. Isolated whole-gene deletions of GALNS have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 8829629, 10479485). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: May 16, 2025

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