NM_130849.4(SLC39A4):c.1174_1195del (p.Glu392fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 28, 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:: RCV001999851.4

Allele description [Variation Report for NM_130849.4(SLC39A4):c.1174_1195del (p.Glu392fs)]

NM_130849.4(SLC39A4):c.1174_1195del (p.Glu392fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

8q24.3

Genomic location:

Preferred name:

NM_130849.4(SLC39A4):c.1174_1195del (p.Glu392fs)

HGVS:

NC_000008.11:g.144414056_144414077del
NG_012234.2:g.7820_7841del
NM_001374839.1:c.892_913del
NM_017767.3:c.1099_1120del
NM_130849.4:c.1174_1195delMANE SELECT
NP_001361768.1:p.Glu298fs
NP_060237.3:p.Glu367fs
NP_570901.3:p.Glu392fs
NC_000008.10:g.145639434_145639455del
NC_000008.10:g.145639440_145639461del

Protein change:

E298fs

Links:

dbSNP: rs1241071909

NCBI 1000 Genomes Browser:

rs1241071909

Molecular consequence:

NM_001374839.1:c.892_913del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_017767.3:c.1099_1120del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130849.4:c.1174_1195del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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PRKAR2B protein kinase cAMP-dependent type II regulatory subunit beta [Homo sapi...
PRKAR2B protein kinase cAMP-dependent type II regulatory subunit beta [Homo sapiens]
Gene ID:5577

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LDHD lactate dehydrogenase D [Homo sapiens]
LDHD lactate dehydrogenase D [Homo sapiens]
Gene ID:197257

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002233583	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 28, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 12955721, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002233583

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 28, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Mutation spectrum of human SLC39A4 in a panel of patients with acrodermatitis enteropathica.

Küry S, Kharfi M, Kamoun R, Taïeb A, Mallet E, Baudon JJ, Glastre C, Michel B, Sebag F, Brooks D, Schuster V, Scoul C, Dréno B, Bézieau S, Moisan JP.

Hum Mutat. 2003 Oct;22(4):337-8.

PubMed [citation]

PMID:: 12955721

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, SCV002233583.3

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

Description

This sequence change creates a premature translational stop signal (p.Glu392Profs*84) in the SLC39A4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC39A4 are known to be pathogenic (PMID: 12955721). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with SLC39A4-related conditions. ClinVar contains an entry for this variant (Variation ID: 1452525). For these reasons, this variant has been classified as Pathogenic.

#	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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