NM_001875.5(CPS1):c.2771C>T (p.Thr924Ile) AND Congenital hyperammonemia, type I

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Dec 1, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV001837207.4

Allele description [Variation Report for NM_001875.5(CPS1):c.2771C>T (p.Thr924Ile)]

NM_001875.5(CPS1):c.2771C>T (p.Thr924Ile)

Gene:

CPS1:carbamoyl-phosphate synthase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q34

Genomic location:

Preferred name:

NM_001875.5(CPS1):c.2771C>T (p.Thr924Ile)

HGVS:

NC_000002.12:g.210637785C>T
NG_008285.1:g.165101C>T
NM_001122633.3:c.2771C>T
NM_001369256.1:c.2804C>T
NM_001369257.1:c.2771C>T
NM_001875.5:c.2771C>TMANE SELECT
NP_001116105.2:p.Thr924Ile
NP_001356185.1:p.Thr935Ile
NP_001356186.1:p.Thr924Ile
NP_001866.2:p.Thr924Ile
LRG_336t1:c.2771C>T
LRG_336:g.165101C>T
NC_000002.11:g.211502509C>T
NM_001875.4:c.2771C>T
NR_161225.1:n.3680C>T
NR_163592.1:n.1927C>T

Protein change:

T924I

Links:

dbSNP: rs150463750

NCBI 1000 Genomes Browser:

rs150463750

Molecular consequence:

NM_001122633.3:c.2771C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369256.1:c.2804C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369257.1:c.2771C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001875.5:c.2771C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_161225.1:n.3680C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_163592.1:n.1927C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Congenital hyperammonemia, type I
Synonyms:: CPS I DEFICIENCY; Hyperammonemia due to carbamoyl phosphate synthetase 1 deficiency; CPS 1 deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009376; MedGen: C4082171; Orphanet: 147; OMIM: 237300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002097696	New York Genome Center - CSER-NYCKidSeq	criteria provided, single submitter (NYGC Assertion Criteria 2020)	Uncertain significance (Jul 10, 2020)	germline	clinical testing	Citation Link,
SCV003525896	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (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

SCV002097696

New York Genome Center - CSER-NYCKidSeq

criteria provided, single submitter

(NYGC Assertion Criteria 2020)

Uncertain significance
(Jul 10, 2020)

germline

clinical testing

Citation Link,

SCV003525896

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(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	1	not provided	not provided	1	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 New York Genome Center - CSER-NYCKidSeq, SCV002097696.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	1	not provided	not provided		1	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003525896.2

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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