NM_130849.4(SLC39A4):c.1193_1199dup (p.Trp401fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 28, 2022
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:: RCV001388616.4

Allele description [Variation Report for NM_130849.4(SLC39A4):c.1193_1199dup (p.Trp401fs)]

NM_130849.4(SLC39A4):c.1193_1199dup (p.Trp401fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

8q24.3

Genomic location:

Preferred name:

NM_130849.4(SLC39A4):c.1193_1199dup (p.Trp401fs)

HGVS:

NC_000008.11:g.144414047TGGGCTG[3]
NG_012234.2:g.7832AGCCCAC[3]
NM_001374839.1:c.911_917dup
NM_017767.3:c.1118_1124dup
NM_130849.4:c.1193_1199dupMANE SELECT
NP_001361768.1:p.Trp307fs
NP_060237.3:p.Trp376fs
NP_570901.3:p.Trp401fs
NC_000008.10:g.145639429_145639430insGTGGGCT
NC_000008.10:g.145639431TGGGCTG[3]

Protein change:

W307fs

Links:

dbSNP: rs1285049551

NCBI 1000 Genomes Browser:

rs1285049551

Molecular consequence:

NM_001374839.1:c.911_917dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_017767.3:c.1118_1124dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_130849.4:c.1193_1199dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001589686	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 28, 2022)	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

SCV001589686

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 28, 2022)

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, SCV001589686.3

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with SLC39A4-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.001%). This sequence change creates a premature translational stop signal (p.Trp401Alafs*19) 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).

#	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

ClinVar

Relating variation to medicine