NM_130849.4(SLC39A4):c.251C>T (p.Pro84Leu) AND Hereditary acrodermatitis enteropathica

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Jul 10, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000365601.9

Allele description [Variation Report for NM_130849.4(SLC39A4):c.251C>T (p.Pro84Leu)]

NM_130849.4(SLC39A4):c.251C>T (p.Pro84Leu)

Gene:

SLC39A4:solute carrier family 39 member 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q24.3

Genomic location:

Preferred name:

NM_130849.4(SLC39A4):c.251C>T (p.Pro84Leu)

Other names:

NM_017767.2(SLC39A4):c.176C>T(p.Pro59Leu); NM_130849.3(SLC39A4):c.251C>T(p.Pro84Leu)

HGVS:

NC_000008.11:g.144416033G>A
NG_012234.2:g.5858C>T
NM_001374839.1:c.192+565C>T
NM_017767.3:c.176C>T
NM_130849.4:c.251C>TMANE SELECT
NP_060237.3:p.Pro59Leu
NP_570901.3:p.Pro84Leu
NC_000008.10:g.145641417G>A
NM_130849.2:c.251C>T
NM_130849.3:c.251C>T

Protein change:

P59L

Links:

dbSNP: rs117535951

NCBI 1000 Genomes Browser:

rs117535951

Molecular consequence:

NM_001374839.1:c.192+565C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_017767.3:c.176C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_130849.4:c.251C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary acrodermatitis enteropathica (AEZ)
Synonyms:: Acrodermatitis enteropathica; Acrodermatitis enteropathica zinc deficiency type; Brandt syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008713; MedGen: C0221036; Orphanet: 37; OMIM: 201100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000472588	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification 20161018)	Likely benign (Jun 14, 2016)	germline	clinical testing	ICSL_Variant_Classification_20161018.pdf, Citation Link,
SCV000803491	SIB Swiss Institute of Bioinformatics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (May 31, 2018)	unknown	curation	PubMed (1) [See all records that cite this PMID]
SCV001762908	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 10, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002083130	Natera, Inc.	no assertion criteria provided	Benign (Oct 25, 2019)	germline	clinical testing

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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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	curation
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

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 Illumina Laboratory Services, Illumina, SCV000472588.2

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

#	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

From SIB Swiss Institute of Bioinformatics, SCV000803491.1

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

Description

This variant is interpreted as a Benign - Stand Alone, for Acrodermatitis enteropathica, zinc-deficiency type, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BA1 =>Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. BS1 => Allele frequency is greater than expected for disorder. BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.

#	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

From Genome-Nilou Lab, SCV001762908.1

#	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	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV002083130.1

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

#	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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