NM_000046.5(ARSB):c.160G>A (p.Asp54Asn) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 8, 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:: RCV004719941.1

Allele description [Variation Report for NM_000046.5(ARSB):c.160G>A (p.Asp54Asn)]

NM_000046.5(ARSB):c.160G>A (p.Asp54Asn)

Genes:

LOC129994126:ATAC-STARR-seq lymphoblastoid silent region 16127 [Gene]
ARSB:arylsulfatase B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q14.1

Genomic location:

Preferred name:

NM_000046.5(ARSB):c.160G>A (p.Asp54Asn)

HGVS:

NC_000005.10:g.78985089C>T
NG_007089.1:g.6446G>A
NM_000046.3:c.160G>A
NM_000046.5:c.160G>AMANE SELECT
NM_198709.3:c.160G>A
NP_000037.2:p.Asp54Asn
NP_942002.1:p.Asp54Asn
NC_000005.9:g.78280912C>T
NM_000046.4:c.160G>A

Protein change:

D54N

Links:

dbSNP: rs1554032216

NCBI 1000 Genomes Browser:

rs1554032216

Molecular consequence:

NM_000046.5:c.160G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_198709.3:c.160G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005325519	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Sep 8, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005325519

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Sep 8, 2023)

germline

clinical testing

Citation Link

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	clinical testing

Details of each submission

From GeneDx, SCV005325519.1

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

Description

Expression studies found D54N is associated with a decrease in enzyme activity similar to that caused by loss of function variants in this gene (Uttarilli et al., 2017); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17458871, 27826022, 26609033)

#	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: Oct 8, 2024

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