NM_003052.5(SLC34A1):c.460_480dup (p.Ile154_Val160dup) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 27, 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:: RCV001851833.4

Allele description [Variation Report for NM_003052.5(SLC34A1):c.460_480dup (p.Ile154_Val160dup)]

NM_003052.5(SLC34A1):c.460_480dup (p.Ile154_Val160dup)

Gene:

SLC34A1:solute carrier family 34 member 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

5q35.3

Genomic location:

Preferred name:

NM_003052.5(SLC34A1):c.460_480dup (p.Ile154_Val160dup)

HGVS:

NC_000005.10:g.177386494_177386514dup
NG_016223.1:g.7064_7084dup
NM_001167579.2:c.460_480dup
NM_003052.5:c.460_480dupMANE SELECT
NP_001161051.1:p.Ile154_Val160dup
NP_003043.3:p.Ile154_Val160dup
NC_000005.9:g.176813493_176813494insGATCCTGGTGACCGTGCTGGT
NC_000005.9:g.176813495_176813515dup
NM_003052.4:c.460_480dup

Note:

NCBI staff reviewed the sequence information reported in PubMed 20335586 Fig. 2A to determine the location of this allele on the current reference sequence.

Links:

OMIM: 182309.0003; dbSNP: rs1554095263

NCBI 1000 Genomes Browser:

rs1554095263

Molecular consequence:

NM_001167579.2:c.460_480dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_003052.5:c.460_480dup - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002250188	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 27, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 20335586, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002250188

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 27, 2021)

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

A loss-of-function mutation in NaPi-IIa and renal Fanconi's syndrome.

Magen D, Berger L, Coady MJ, Ilivitzki A, Militianu D, Tieder M, Selig S, Lapointe JY, Zelikovic I, Skorecki K.

N Engl J Med. 2010 Mar 25;362(12):1102-9. doi: 10.1056/NEJMoa0905647.

PubMed [citation]

PMID:: 20335586

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002250188.2

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

Description

This variant, c.460_480dup, results in the insertion of 7 amino acid(s) to the SLC34A1 protein (p.Ile154_Val160dup), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has been observed in individual(s) with SLC34A1-related conditions (PMID: 20335586). ClinVar contains an entry for this variant (Variation ID: 12933). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects SLC34A1 function (PMID: 20335586). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Mar 26, 2023

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