NM_177550.5(SLC13A5):c.446T>C (p.Val149Ala) AND Developmental and epileptic encephalopathy, 25

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 30, 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:: RCV002005692.4

Allele description [Variation Report for NM_177550.5(SLC13A5):c.446T>C (p.Val149Ala)]

NM_177550.5(SLC13A5):c.446T>C (p.Val149Ala)

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.446T>C (p.Val149Ala)

HGVS:

NC_000017.11:g.6703979A>G
NG_034220.1:g.14443T>C
NM_001143838.3:c.446T>C
NM_001284509.2:c.395T>C
NM_001284510.2:c.317T>C
NM_177550.5:c.446T>CMANE SELECT
NP_001137310.1:p.Val149Ala
NP_001271438.1:p.Val132Ala
NP_001271439.1:p.Val106Ala
NP_808218.1:p.Val149Ala
LRG_1020:g.14443T>C
NC_000017.10:g.6607298A>G

Protein change:

V106A

Links:

dbSNP: rs761377416

NCBI 1000 Genomes Browser:

rs761377416

Molecular consequence:

NM_001143838.3:c.446T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001284509.2:c.395T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001284510.2:c.317T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_177550.5:c.446T>C - 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

Recent activity

Clear Turn Off Turn On

Klebsiella pneumoniae strain 2020-314 plasmid pKGMAR-2020-314.1, complete sequen...
Klebsiella pneumoniae strain 2020-314 plasmid pKGMAR-2020-314.1, complete sequence
gi|2805267462|ref|NZ_CP144894.1|

Nucleotide
Escherichia coli strain LQN1008 9, whole genome shotgun sequence
Escherichia coli strain LQN1008 9, whole genome shotgun sequence
gi|2806027891|ref|NZ_JBHFVR01000000 gnl|WGS:NZ_JBHFVR01|9

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002273798	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 30, 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

SCV002273798

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 30, 2021)

germline

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	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002273798.3

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

Description

This variant has not been reported in the literature in individuals affected with SLC13A5-related conditions. This variant is present in population databases (rs761377416, gnomAD 0.02%). This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 149 of the SLC13A5 protein (p.Val149Ala). 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: "Benign"; Align-GVGD: "Class C25"). 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: Sep 29, 2024

ClinVar

Relating variation to medicine