NM_004174.4(SLC9A3):c.2376del (p.Tyr793fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 24, 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:: RCV003695559.1

Allele description [Variation Report for NM_004174.4(SLC9A3):c.2376del (p.Tyr793fs)]

NM_004174.4(SLC9A3):c.2376del (p.Tyr793fs)

Genes:

SLC9A3-AS1:SLC9A3 antisense RNA 1 [Gene - HGNC]
SLC9A3:solute carrier family 9 member A3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5p15.33

Genomic location:

Preferred name:

NM_004174.4(SLC9A3):c.2376del (p.Tyr793fs)

HGVS:

NC_000005.10:g.475010del
NG_046804.1:g.100421del
NM_001284351.3:c.2349del
NM_004174.4:c.2376delMANE SELECT
NP_001271280.1:p.Tyr784fs
NP_004165.2:p.Tyr793fs
NC_000005.9:g.475123del
NC_000005.9:g.475125del

Protein change:

Y784fs

Molecular consequence:

NM_001284351.3:c.2349del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004174.4:c.2376del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV004449869	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 24, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26358773, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004449869

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 24, 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

Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea.

Janecke AR, Heinz-Erian P, Yin J, Petersen BS, Franke A, Lechner S, Fuchs I, Melancon S, Uhlig HH, Travis S, Marinier E, Perisic V, Ristic N, Gerner P, Booth IW, Wedenoja S, Baumgartner N, Vodopiutz J, Frechette-Duval MC, De Lafollie J, Persad R, Warner N, et al.

Hum Mol Genet. 2015 Dec 1;24(23):6614-23. doi: 10.1093/hmg/ddv367. Epub 2015 Sep 10.

PubMed [citation]

PMID:: 26358773
PMCID:: PMC4634371

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 Invitae, SCV004449869.1

#	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 SLC9A3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr793Thrfs*9) in the SLC9A3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC9A3 are known to be pathogenic (PMID: 26358773).

#	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: Feb 28, 2024

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