NM_177550.5(SLC13A5):c.1558C>T (p.Leu520Phe) AND Developmental and epileptic encephalopathy, 25

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 19, 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:: RCV001876422.5

Allele description

NM_177550.5(SLC13A5):c.1558C>T (p.Leu520Phe)

Gene:

SLC13A5:solute carrier family 13 member 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_177550.5(SLC13A5):c.1558C>T (p.Leu520Phe)

HGVS:

NC_000017.11:g.6687546G>A
NG_034220.1:g.30876C>T
NM_001143838.3:c.1438-1208C>T
NM_001284509.2:c.1507C>T
NM_001284510.2:c.1429C>T
NM_177550.5:c.1558C>TMANE SELECT
NP_001271438.1:p.Leu503Phe
NP_001271439.1:p.Leu477Phe
NP_808218.1:p.Leu520Phe
LRG_1020:g.30876C>T
NC_000017.10:g.6590865G>A

Protein change:

L477F

Links:

dbSNP: rs779246920

NCBI 1000 Genomes Browser:

rs779246920

Molecular consequence:

NM_001143838.3:c.1438-1208C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001284509.2:c.1507C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001284510.2:c.1429C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_177550.5:c.1558C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 25 (DEE25)
Synonyms:: Epileptic encephalopathy, early infantile, 25; Developmental and epileptic encephalopathy 25, with amelogenesis imperfecta; Epileptic encephalopathy, early infantile, 25, with amelogenesis imperfecta
Identifiers:: MONDO: MONDO:0014392; MedGen: C4014621; Orphanet: 442835; OMIM: 615905

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NPC1-like intracellular cholesterol transporter 1 isoform X1 [Homo sapiens]
NPC1-like intracellular cholesterol transporter 1 isoform X1 [Homo sapiens]
gi|2462613938|ref|XP_054213993.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002126611	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 19, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002126611

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 19, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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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

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, SCV002126611.3

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with SLC13A5-related conditions. This variant is present in population databases (rs779246920, ExAC 0.009%). This sequence change replaces leucine with phenylalanine at codon 520 of the SLC13A5 protein (p.Leu520Phe). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and phenylalanine.

#	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 5, 2024

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