NM_004482.4(GALNT3):c.803dup (p.Thr269fs) AND Tumoral calcinosis, hyperphosphatemic, familial, 1

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 22, 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:: RCV000008243.5

Allele description [Variation Report for NM_004482.4(GALNT3):c.803dup (p.Thr269fs)]

NM_004482.4(GALNT3):c.803dup (p.Thr269fs)

Gene:

GALNT3:polypeptide N-acetylgalactosaminyltransferase 3 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

2q24.3

Genomic location:

Preferred name:

NM_004482.4(GALNT3):c.803dup (p.Thr269fs)

HGVS:

NC_000002.12:g.165761940dup
NG_012069.1:g.37354dup
NM_004482.4:c.803dupMANE SELECT
NP_004473.2:p.Thr269fs
NC_000002.11:g.166618449_166618450insG
NC_000002.11:g.166618450dup
NM_004482.3:c.803dup

Note:

NCBI staff reviewed the sequence information reported in PubMed 17311862 Fig. 1B to determine the location of this allele on the current reference sequence.

Protein change:

T269fs

Links:

OMIM: 601756.0010; dbSNP: rs766750282

NCBI 1000 Genomes Browser:

rs766750282

Molecular consequence:

NM_004482.4:c.803dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Tumoral calcinosis, hyperphosphatemic, familial, 1
Synonyms:: CALCINOSIS, TUMORAL, WITH HYPERPHOSPHATEMIA; LIPOCALCINOGRANULOMATOSIS; MORBUS TEUTSCHLAENDER; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0100252; MedGen: C4692564; Orphanet: 53715; OMIM: 211900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000028450	OMIM	no assertion criteria provided	Pathogenic (May 1, 2007)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002811732	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 22, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000028450

OMIM

no assertion criteria provided

Pathogenic
(May 1, 2007)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

SCV002811732

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 22, 2022)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel GALNT3 mutations causing hyperostosis-hyperphosphatemia syndrome result in low intact fibroblast growth factor 23 concentrations.

Ichikawa S, Guigonis V, Imel EA, Courouble M, Heissat S, Henley JD, Sorenson AH, Petit B, Lienhardt A, Econs MJ.

J Clin Endocrinol Metab. 2007 May;92(5):1943-7. Epub 2007 Feb 20.

PubMed [citation]

PMID:: 17311862

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From OMIM, SCV000028450.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a 5-year-old French boy with hyperostosis-hyperphosphatemia syndrome (HFTC1; 211900), Ichikawa et al. (2007) identified compound heterozygosity for 2 mutations in the GALNT3 gene: a 1-bp insertion (803_804insC) in exon 3, and a splice site mutation, IVS8+1G-A (601756.0011). The boy presented with painful cortical lesions in his leg, and radiographs of the affected bone showed diaphyseal hyperostosis. The lesional tissue comprised trabeculae of immature, woven bone surrounded by fibrous tissue. Intact FGF23 level in the patient was low normal, whereas C-terminal FGF23 was elevated, a pattern similar that in tumoral calcinosis. The patient's parents and brother were heterozygous for one of the mutations and had no biochemical abnormalities. Ichikawa et al. (2007) suggested that hyperostosis-hyperphosphatemia syndrome and familial tumoral calcinosis are different manifestations of the same disorder.

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

From Fulgent Genetics, Fulgent Genetics, SCV002811732.1

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

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

Last Updated: Sep 29, 2024

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