U.S. flag

An official website of the United States government

NM_130849.4(SLC39A4):c.977-1G>A AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 15, 2021
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:
RCV002005676.6

Allele description [Variation Report for NM_130849.4(SLC39A4):c.977-1G>A]

NM_130849.4(SLC39A4):c.977-1G>A

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.977-1G>A
HGVS:
  • NC_000008.11:g.144414435C>T
  • NG_012234.2:g.7456G>A
  • NG_012234.3:g.7409G>A
  • NG_115586.1:g.653C>T
  • NM_001374839.1:c.695-1G>A
  • NM_017767.3:c.902-1G>A
  • NM_130849.4:c.977-1G>AMANE SELECT
  • NC_000008.10:g.145639819C>T
Links:
dbSNP: rs2130798128
NCBI 1000 Genomes Browser:
rs2130798128
Molecular consequence:
  • NM_001374839.1:c.695-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_017767.3:c.902-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_130849.4:c.977-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002277213Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Jan 15, 2021) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

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
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002277213.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with SLC39A4-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 5 of the SLC39A4 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SLC39A4 are known to be pathogenic (PMID: 12955721).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024