NM_020708.5(SLC12A5):c.3101G>A (p.Ser1034Asn) AND Developmental and epileptic encephalopathy, 34

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 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:: RCV002017774.6

Allele description [Variation Report for NM_020708.5(SLC12A5):c.3101G>A (p.Ser1034Asn)]

NM_020708.5(SLC12A5):c.3101G>A (p.Ser1034Asn)

Gene:

SLC12A5:solute carrier family 12 member 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q13.12

Genomic location:

Preferred name:

NM_020708.5(SLC12A5):c.3101G>A (p.Ser1034Asn)

HGVS:

NC_000020.11:g.46056555G>A
NG_046341.1:g.39866G>A
NM_001134771.2:c.3170G>A
NM_020708.5:c.3101G>AMANE SELECT
NP_001128243.1:p.Ser1057Asn
NP_065759.1:p.Ser1034Asn
NC_000020.10:g.44685194G>A

Protein change:

S1034N

Links:

dbSNP: rs750612388

NCBI 1000 Genomes Browser:

rs750612388

Molecular consequence:

NM_001134771.2:c.3170G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020708.5:c.3101G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 34 (DEE34)
Synonyms:: Early infantile epileptic encephalopathy 34
Identifiers:: MONDO: MONDO:0014718; MedGen: C4225257; Orphanet: 293181; OMIM: 616645

Recent activity

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Saccharomyces cerevisiae S288C Yhp1p (YHP1), partial mRNA
Saccharomyces cerevisiae S288C Yhp1p (YHP1), partial mRNA
gi|398366606|ref|NM_001180759.3|

Nucleotide
hsc70-interacting protein [Rattus norvegicus]
hsc70-interacting protein [Rattus norvegicus]
gi|13592093|ref|NP_112384.1|

Protein
Rattus norvegicus clone CH230-480G5, WORKING DRAFT SEQUENCE, 3 ordered pieces
Rattus norvegicus clone CH230-480G5, WORKING DRAFT SEQUENCE, 3 ordered pieces
gi|237874750|gnl|bcmhgsc|project_kc ylor|gb|AC136183.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002302981	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 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

SCV002302981

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 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, SCV002302981.3

#	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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SLC12A5 protein function. This variant has not been reported in the literature in individuals with SLC12A5-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with asparagine at codon 1034 of the SLC12A5 protein (p.Ser1034Asn). The serine residue is moderately conserved and there is a small physicochemical difference between serine and asparagine.

#	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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