NM_000047.3(ARSL):c.1759G>A (p.Asp587Asn) AND Chondrodysplasia punctata, brachytelephalangic, autosomal

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 29, 2023
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:: RCV002237994.6

Allele description [Variation Report for NM_000047.3(ARSL):c.1759G>A (p.Asp587Asn)]

NM_000047.3(ARSL):c.1759G>A (p.Asp587Asn)

Gene:

ARSL:arylsulfatase L [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp22.33

Genomic location:

Preferred name:

NM_000047.3(ARSL):c.1759G>A (p.Asp587Asn)

HGVS:

NC_000023.11:g.2934843C>T
NG_007091.1:g.34428G>A
NM_000047.3:c.1759G>AMANE SELECT
NM_001282628.2:c.1834G>A
NM_001282631.2:c.1597G>A
NM_001369079.1:c.1786G>A
NM_001369080.1:c.1834G>A
NP_000038.2:p.Asp587Asn
NP_001269557.1:p.Asp612Asn
NP_001269560.2:p.Asp533Asn
NP_001356008.1:p.Asp596Asn
NP_001356009.1:p.Asp612Asn
NC_000023.10:g.2852884C>T

Protein change:

D533N

Links:

dbSNP: rs753500701

NCBI 1000 Genomes Browser:

rs753500701

Molecular consequence:

NM_000047.3:c.1759G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282628.2:c.1834G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282631.2:c.1597G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369079.1:c.1786G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001369080.1:c.1834G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Chondrodysplasia punctata, brachytelephalangic, autosomal
Synonyms:: BRACHYTELEPHALANGIC CHONDRODYSPLASIA PUNCTATA
Identifiers:: MONDO: MONDO:0011238; MedGen: C1844853; OMIM: 602497

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AKRDC1 (14)
Protein
zinc finger protein 177 [Homo sapiens]
zinc finger protein 177 [Homo sapiens]
gi|4508009|ref|NP_003442.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002511330	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 29, 2023)	germline	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

SCV002511330

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 29, 2023)

germline

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002511330.3

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

Description

This variant has not been reported in the literature in individuals affected with ARSE-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ARSE protein function. ClinVar contains an entry for this variant (Variation ID: 1683175). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 587 of the ARSE protein (p.Asp587Asn).

#	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: Sep 29, 2024

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