NM_001905.4(CTPS1):c.137A>G (p.Asp46Gly) AND Severe combined immunodeficiency due to CTPS1 deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 13, 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:: RCV001988267.6

Allele description [Variation Report for NM_001905.4(CTPS1):c.137A>G (p.Asp46Gly)]

NM_001905.4(CTPS1):c.137A>G (p.Asp46Gly)

Gene:

CTPS1:CTP synthase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_001905.4(CTPS1):c.137A>G (p.Asp46Gly)

HGVS:

NC_000001.11:g.40983427A>G
NG_034208.1:g.9129A>G
NM_001905.4:c.137A>GMANE SELECT
NP_001896.2:p.Asp46Gly
LRG_1229t1:c.137A>G
LRG_1229:g.9129A>G
LRG_1229p1:p.Asp46Gly
NC_000001.10:g.41449099A>G
NR_125440.2:n.284A>G

Protein change:

D46G

Links:

dbSNP: rs757447163

NCBI 1000 Genomes Browser:

rs757447163

Molecular consequence:

NM_001905.4:c.137A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_125440.2:n.284A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Severe combined immunodeficiency due to CTPS1 deficiency
Synonyms:: Immunodeficiency 24
Identifiers:: MONDO: MONDO:0014391; MedGen: C4014617; Orphanet: 420573; OMIM: 615897

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002262280	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 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

SCV002262280

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 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, SCV002262280.3

#	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 aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 46 of the CTPS1 protein (p.Asp46Gly). This variant is present in population databases (rs757447163, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with CTPS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1481234). 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: Sep 29, 2024

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