NM_001024845.3(SLC6A9):c.361A>G (p.Ile121Val) AND Atypical glycine encephalopathy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 1, 2023
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:: RCV002633621.3

Allele description [Variation Report for NM_001024845.3(SLC6A9):c.361A>G (p.Ile121Val)]

NM_001024845.3(SLC6A9):c.361A>G (p.Ile121Val)

Gene:

SLC6A9:solute carrier family 6 member 9 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.1

Genomic location:

Preferred name:

NM_001024845.3(SLC6A9):c.361A>G (p.Ile121Val)

HGVS:

NC_000001.11:g.44008582T>C
NG_050929.1:g.27911A>G
NM_001024845.3:c.361A>GMANE SELECT
NM_001261380.2:c.373A>G
NM_001328626.2:c.28A>G
NM_001328627.1:c.298A>G
NM_001328628.1:c.166A>G
NM_001328629.1:c.361A>G
NM_001328630.2:c.28A>G
NM_006934.4:c.418A>G
NM_201649.4:c.580A>G
NP_001020016.1:p.Ile121Val
NP_001248309.1:p.Ile125Val
NP_001315555.1:p.Ile10Val
NP_001315556.1:p.Ile100Val
NP_001315557.1:p.Ile56Val
NP_001315558.1:p.Ile121Val
NP_001315559.1:p.Ile10Val
NP_008865.2:p.Ile140Val
NP_964012.2:p.Ile194Val
NC_000001.10:g.44474254T>C
NR_048548.2:n.448A>G
NR_048549.1:n.344A>G

Protein change:

I100V

Molecular consequence:

NM_001024845.3:c.361A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001261380.2:c.373A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001328626.2:c.28A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001328627.1:c.298A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001328628.1:c.166A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001328629.1:c.361A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001328630.2:c.28A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006934.4:c.418A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_201649.4:c.580A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_048548.2:n.448A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Atypical glycine encephalopathy
Synonyms:: Glycine encephalopathy with normal serum glycine
Identifiers:: MONDO: MONDO:0015010; MedGen: C4310943; OMIM: 617301

Recent activity

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Homo sapiens nuclear receptor subfamily 5 group A member 2 (NR5A2), RefSeqGene o...
Homo sapiens nuclear receptor subfamily 5 group A member 2 (NR5A2), RefSeqGene on chromosome 1
gi|1039673930|ref|NG_050913.1|

Nucleotide
histone deacetylase 5 isoform X4 [Homo sapiens]
histone deacetylase 5 isoform X4 [Homo sapiens]
gi|2462552201|ref|XP_054170593.1|

Protein
Chlorophyllum sphaerosporum voucher HMAS 71683 RNA polymerase second largest sub...
Chlorophyllum sphaerosporum voucher HMAS 71683 RNA polymerase second largest subunit (rpb2) gene, partial cds
gi|1384892682|gb|MG742073.1|

Nucleotide
Chlorophyllum africanum voucher PREM 62140 RNA polymerase second largest subunit...
Chlorophyllum africanum voucher PREM 62140 RNA polymerase second largest subunit (rpb2) gene, partial cds
gi|1384892676|gb|MG742070.1|

Nucleotide
Chlorophyllum subrhacodes voucher Z.W. Ge 3411 RNA polymerase second largest sub...
Chlorophyllum subrhacodes voucher Z.W. Ge 3411 RNA polymerase second largest subunit (rpb2) gene, partial cds
gi|1384892684|gb|MG742074.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003515725	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 1, 2023)	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

SCV003515725

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 1, 2023)

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, SCV003515725.2

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

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 194 of the SLC6A9 protein (p.Ile194Val). This variant is present in population databases (rs753932866, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with SLC6A9-related conditions. ClinVar contains an entry for this variant (Variation ID: 2196374). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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: Nov 10, 2024

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