NM_177550.5(SLC13A5):c.485_487dup (p.Thr162dup) AND Developmental and epileptic encephalopathy, 25

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 19, 2022
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:: RCV001301836.6

Allele description [Variation Report for NM_177550.5(SLC13A5):c.485_487dup (p.Thr162dup)]

NM_177550.5(SLC13A5):c.485_487dup (p.Thr162dup)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_177550.5(SLC13A5):c.485_487dup (p.Thr162dup)

HGVS:

NC_000017.11:g.6703939_6703941dup
NG_034220.1:g.14482_14484dup
NM_001143838.3:c.485_487dup
NM_001284509.2:c.434_436dup
NM_001284510.2:c.356_358dup
NM_177550.5:c.485_487dupMANE SELECT
NP_001137310.1:p.Thr162dup
NP_001271438.1:p.Thr145dup
NP_001271439.1:p.Thr119dup
NP_808218.1:p.Thr162dup
LRG_1020:g.14482_14484dup
NC_000017.10:g.6607256_6607257insTTG
NC_000017.10:g.6607258_6607260dup
NM_177550.4:c.485_487dupCAA

Links:

dbSNP: rs748215544

NCBI 1000 Genomes Browser:

rs748215544

Molecular consequence:

NM_001143838.3:c.485_487dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001284509.2:c.434_436dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001284510.2:c.356_358dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_177550.5:c.485_487dup - inframe_insertion - [Sequence Ontology: SO:0001821]

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

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
SCV001491019	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 19, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002055674	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 15, 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

SCV001491019

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 19, 2022)

germline

clinical testing

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

SCV002055674

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 15, 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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001491019.3

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

Description

This variant, c.485_487dup, results in the insertion of 1 amino acid(s) of the SLC13A5 protein (p.Thr162dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs748215544, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with SLC13A5-related conditions. ClinVar contains an entry for this variant (Variation ID: 546412). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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

From Genome-Nilou Lab, SCV002055674.1

#	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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine