NM_001543.5(NDST1):c.39C>G (p.His13Gln) AND Intellectual disability, autosomal recessive 46

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 11, 2017
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:: RCV000678273.2

Allele description [Variation Report for NM_001543.5(NDST1):c.39C>G (p.His13Gln)]

NM_001543.5(NDST1):c.39C>G (p.His13Gln)

Gene:

NDST1:N-deacetylase and N-sulfotransferase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q33.1

Genomic location:

Preferred name:

NM_001543.5(NDST1):c.39C>G (p.His13Gln)

HGVS:

NC_000005.10:g.150521293C>G
NG_041806.1:g.28516C>G
NM_001301063.2:c.39C>G
NM_001543.5:c.39C>GMANE SELECT
NP_001287992.1:p.His13Gln
NP_001534.1:p.His13Gln
NC_000005.9:g.149900855C>G
NM_001543.4:c.39C>G

Protein change:

H13Q

Links:

dbSNP: rs777877507

NCBI 1000 Genomes Browser:

rs777877507

Molecular consequence:

NM_001301063.2:c.39C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001543.5:c.39C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Intellectual disability, autosomal recessive 46 (MRT46)
Synonyms:: INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 46
Identifiers:: MONDO: MONDO:0014499; MedGen: C4015283; Orphanet: 88616; OMIM: 616116

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000804329	Geisinger Autism and Developmental Medicine Institute, Geisinger Health System	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 11, 2017)	paternal	provider interpretation, 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

SCV000804329

Geisinger Autism and Developmental Medicine Institute, Geisinger Health System

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 11, 2017)

paternal

provider interpretation, 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	paternal	unknown	1	not provided	not provided	1	not provided	clinical testing, provider interpretation

Citations

PubMed

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 Geisinger Autism and Developmental Medicine Institute, Geisinger Health System, SCV000804329.2

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

Description

This 5-year old male with a history of global developmental delay, hyperkinesis, and mixed receptive-expressive language disorder was found to be compound heterozygous for two variants in the NDST1 gene. This particular variant has been reported in the non-Finnish European population at a frequency of 0.0009%. Computational models are inconsistent. This variant is not in either the heparan sulfate N-deacetylase 1 domain or the sulfotransferase domain.

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

Last Updated: Aug 5, 2023

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