NM_012434.5(SLC17A5):c.409del (p.Met137fs) AND Salla disease

Germline classification:: Pathogenic/Likely pathogenic (5 submissions)
Last evaluated:: Oct 20, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000185578.10

Allele description [Variation Report for NM_012434.5(SLC17A5):c.409del (p.Met137fs)]

NM_012434.5(SLC17A5):c.409del (p.Met137fs)

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.409del (p.Met137fs)

HGVS:

NC_000006.12:g.73641810del
NG_008272.1:g.17208del
NM_012434.5:c.409delMANE SELECT
NP_036566.1:p.Met137fs
NC_000006.11:g.74351530del
NC_000006.11:g.74351533del
NM_012434.4:c.409del
NM_012434.4:c.409delA

Protein change:

M137fs

Links:

dbSNP: rs794729653

NCBI 1000 Genomes Browser:

rs794729653

Molecular consequence:

NM_012434.5:c.409del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000238478	Division of Human Genetics, Children's Hospital of Philadelphia - CSER-PediSeq	no assertion criteria provided	Likely pathogenic (Jul 17, 2014)	germline	research	PubMed (2) [See all records that cite these PMIDs] 10581036, 15805149
SCV000486112	Counsyl	criteria provided, single submitter (Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))	Likely pathogenic (Mar 30, 2016)	unknown	clinical testing	mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf, Citation Link,
SCV001222701	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 8, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 10581036, 10947946, 15172001, 28492532
SCV002027579	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004201209	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 20, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing, research
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical, morphological, and molecular aspects of sialic acid storage disease manifesting in utero.

Froissart R, Cheillan D, Bouvier R, Tourret S, Bonnet V, Piraud M, Maire I.

J Med Genet. 2005 Nov;42(11):829-36. Epub 2005 Apr 1.

PubMed [citation]

PMID:: 15805149
PMCID:: PMC1735939

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

See all PubMed Citations (6)

Details of each submission

From Division of Human Genetics, Children's Hospital of Philadelphia - CSER-PediSeq, SCV000238478.1

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

Description

The SLC17A5 gene variant (c.409delA; p.Met137Cysfs*3) identified in this patient is a novel frameshift variant, which results in a truncated protein, considered a pathogenic variant .

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Counsyl, SCV000486112.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Invitae, SCV001222701.5

#	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.Met137Cysfs*3) 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. ClinVar contains an entry for this variant (Variation ID: 203395). 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

From Genome-Nilou Lab, SCV002027579.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004201209.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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