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NM_016579.4(CD320):c.334G>A (p.Gly112Ser) AND Methylmalonic acidemia due to transcobalamin receptor defect

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 4, 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:
RCV001052507.6

Allele description [Variation Report for NM_016579.4(CD320):c.334G>A (p.Gly112Ser)]

NM_016579.4(CD320):c.334G>A (p.Gly112Ser)

Gene:
CD320:CD320 molecule [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_016579.4(CD320):c.334G>A (p.Gly112Ser)
HGVS:
  • NC_000019.10:g.8304023C>T
  • NG_028124.1:g.9334G>A
  • NM_001165895.2:c.208G>A
  • NM_016579.4:c.334G>AMANE SELECT
  • NP_001159367.1:p.Gly70Ser
  • NP_057663.1:p.Gly112Ser
  • NC_000019.9:g.8368907C>T
  • NM_016579.3:c.334G>A
Protein change:
G112S
Links:
dbSNP: rs948576208
NCBI 1000 Genomes Browser:
rs948576208
Molecular consequence:
  • NM_001165895.2:c.208G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_016579.4:c.334G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Methylmalonic acidemia due to transcobalamin receptor defect
Synonyms:
METHYLMALONIC ACIDEMIA, TCblR TYPE; Methylmalonic aciduria due to transcobalamin receptor defect; METHYLMALONIC ACIDURIA, TRANSIENT, DUE TO TRANSCOBALAMIN RECEPTOR DEFECT
Identifiers:
MONDO: MONDO:0013341; MedGen: C4749905; Orphanet: 280183; OMIM: 613646

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001216719Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 4, 2023) 		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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001216719.4

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

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 848693). This variant has not been reported in the literature in individuals affected with CD320-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 112 of the CD320 protein (p.Gly112Ser).

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

Last Updated: Feb 20, 2024