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NM_000096.4(CP):c.1868T>C (p.Met623Thr) AND Deficiency of ferroxidase

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 19, 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:
RCV002009559.3

Allele description

NM_000096.4(CP):c.1868T>C (p.Met623Thr)

Gene:
CP:ceruloplasmin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q24
Genomic location:
Preferred name:
NM_000096.4(CP):c.1868T>C (p.Met623Thr)
HGVS:
  • NC_000003.12:g.149186729A>G
  • NG_011800.3:g.40317T>C
  • NM_000096.4:c.1868T>CMANE SELECT
  • NP_000087.2:p.Met623Thr
  • NC_000003.11:g.148904516A>G
  • NG_011800.2:g.40317T>C
Protein change:
M623T
Links:
dbSNP: rs1328458846
NCBI 1000 Genomes Browser:
rs1328458846
Molecular consequence:
  • NM_000096.4:c.1868T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Deficiency of ferroxidase (ACEP)
Synonyms:
Aceruloplasminemia; Ceruloplasmin deficiency; Familial apoceruloplasmin deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011426; MedGen: C0878682; Orphanet: 48818; OMIM: 604290; Human Phenotype Ontology: HP:0025498

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002297405Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 19, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Invitae, SCV002297405.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with CP-related conditions. 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 expected to disrupt CP protein function. This variant is not present in population databases (ExAC no frequency). This sequence change replaces methionine with threonine at codon 623 of the CP protein (p.Met623Thr). The methionine residue is moderately conserved and there is a moderate physicochemical difference between methionine and threonine.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 23, 2024