NM_012434.5(SLC17A5):c.267del (p.Pro89_Ile90insTer) AND Salla disease

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 11, 2024
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:: RCV003505921.2

Allele description [Variation Report for NM_012434.5(SLC17A5):c.267del (p.Pro89_Ile90insTer)]

NM_012434.5(SLC17A5):c.267del (p.Pro89_Ile90insTer)

Gene:

SLC17A5:solute carrier family 17 member 5 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6q13

Genomic location:

Preferred name:

NM_012434.5(SLC17A5):c.267del (p.Pro89_Ile90insTer)

HGVS:

NC_000006.12:g.73644433del
NG_008272.1:g.14584del
NM_001382629.1:c.61-2507del
NM_001382630.1:c.267del
NM_001382631.1:c.288del
NM_001382632.1:c.267del
NM_001382633.1:c.267del
NM_001382634.1:c.267del
NM_001382635.1:c.267del
NM_001382636.1:c.61-2507del
NM_012434.5:c.267delMANE SELECT
NP_001369559.1:p.Pro89_Ile90insTer
NP_001369560.1:p.Pro96_Ile97insTer
NP_001369561.1:p.Pro89_Ile90insTer
NP_001369562.1:p.Pro89_Ile90insTer
NP_001369563.1:p.Pro89_Ile90insTer
NP_001369564.1:p.Pro89_Ile90insTer
NP_036566.1:p.Pro89_Ile90insTer
NC_000006.11:g.74354154del
NC_000006.11:g.74354156del

Molecular consequence:

NM_001382630.1:c.267del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001382631.1:c.288del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001382632.1:c.267del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001382633.1:c.267del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001382634.1:c.267del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001382635.1:c.267del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012434.5:c.267del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001382629.1:c.61-2507del - intron variant - [Sequence Ontology: SO:0001627]
NM_001382636.1:c.61-2507del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Salla disease (SD)
Synonyms:: Sialuria, Finnish type; N-acetylneuraminic acid (NANA) storage disease (NSD); Infantile sialic acid storage disorder (ISSD); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011449; MedGen: C1096903; Orphanet: 309334; Orphanet: 834; OMIM: 604369

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004259473	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 11, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 10581036, 10947946, 15172001, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004259473

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 11, 2024)

germline

clinical testing

PubMed (4)
[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 new gene, encoding an anion transporter, is mutated in sialic acid storage diseases.

Verheijen FW, Verbeek E, Aula N, Beerens CE, Havelaar AC, Joosse M, Peltonen L, Aula P, Galjaard H, van der Spek PJ, Mancini GM.

Nat Genet. 1999 Dec;23(4):462-5.

PubMed [citation]

PMID:: 10581036

The spectrum of SLC17A5-gene mutations resulting in free sialic acid-storage diseases indicates some genotype-phenotype correlation.

Aula N, Salomäki P, Timonen R, Verheijen F, Mancini G, Månsson JE, Aula P, Peltonen L.

Am J Hum Genet. 2000 Oct;67(4):832-40. Epub 2000 Aug 17.

PubMed [citation]

PMID:: 10947946
PMCID:: PMC1287888

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004259473.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Ile90*) in the SLC17A5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC17A5 are known to be pathogenic (PMID: 10581036, 10947946, 15172001). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC17A5-related conditions. 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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