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NM_016579.4(CD320):c.256GAG[2] (p.Glu88del) AND Methylmalonic acidemia due to transcobalamin receptor defect

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Jan 26, 2024
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:
RCV000004499.24

Allele description [Variation Report for NM_016579.4(CD320):c.256GAG[2] (p.Glu88del)]

NM_016579.4(CD320):c.256GAG[2] (p.Glu88del)

Gene:
CD320:CD320 molecule [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_016579.4(CD320):c.256GAG[2] (p.Glu88del)
HGVS:
  • NC_000019.10:g.8305035CTC[2]
  • NC_000019.9:g.8369919_8369921del
  • NG_028124.1:g.8314GAG[2]
  • NM_001165895.2:c.143-955GAG[2]
  • NM_016579.4:c.256GAG[2]MANE SELECT
  • NP_057663.1:p.Glu88del
  • NC_000019.10:g.8305035CTC[2]
  • NC_000019.9:g.8369919CTC[2]
  • NC_000019.9:g.8369919_8369921del
  • NC_000019.9:g.8369919_8369921delCTC
  • NM_016579.3:c.262_264del
  • NM_016579.3:c.262_264delGAG
Protein change:
E88del
Links:
OMIM: 606475.0001; dbSNP: rs150384171
NCBI 1000 Genomes Browser:
rs150384171
Molecular consequence:
  • NM_016579.4:c.256GAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001165895.2:c.143-955GAG[2] - intron variant - [Sequence Ontology: SO:0001627]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000024673OMIM
no assertion criteria provided
Pathogenic
(Aug 1, 2010)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000267241Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Mar 18, 2016)
germlinereference population

PubMed (2)
[See all records that cite these PMIDs]

SCV000676997Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jan 26, 2024)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV001140969Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2019)
Benign
(Aug 22, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
East Asiangermlineunknown1not providednot providednot providednot providedreference population

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Bilateral central retinal artery occlusions in an infant with hyperhomocysteinemia.

Karth P, Singh R, Kim J, Costakos D.

J AAPOS. 2012 Aug;16(4):398-400. doi: 10.1016/j.jaapos.2012.04.003. Epub 2012 Jul 18.

PubMed [citation]
PMID:
22819238
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000024673.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In an infant with methylmalonic aciduria (613646) detected by newborn screening, Quadros et al. (2010) identified a homozygous 3-bp deletion (262delGAG) in the CD320 gene, resulting in an in-frame deletion of glu88 in the 3-prime end of the first LDLR type A domain. Newborn screening identified increased blood C3-acylcarnitine levels, and urinary analysis showed moderately elevated MMA. Plasma vitamin B12 and total homocysteine levels were normal. Repeat screening on day 14 of life showed normal C3-acylcarnitine levels and increased MMA; vitamin B12 was administered intramuscularly, and MMA returned to normal. All hematologic parameters were normal, and the mother had no laboratory abnormalities. Studies of patient fibroblasts showed increased levels of MMA and homocysteine compared to control cells, but these levels decreased in the presence of high levels of cobalamin. Patient fibroblasts showed low uptake of transcobalamin-bound cobalamin, but normal conversion to adenosylcobalamin and methylcobalamin, suggesting a defect in the receptor. Insertion of the missing codon by site-directed mutagenesis fully restored TCBLR function. Studies of 4 additional cell lines derived from patients with similar features identified the same mutation; 2 of these additional patients had increased serum homocysteine.

Karth et al. (2012) described a 7-week-old male who presented with bilateral central retinal artery occlusions (CRAO) following incision and drainage of an inguinal lymph node abscess 2 days before and short course of clindamycin preoperatively. Laboratory studies showed elevated serum homocysteine and MMA, indicating a functional deficit of vitamin B12 although serum levels of B12 were normal. DNA analysis of patient fibroblasts revealed homozygosity for an in-frame deletion of glu88 (262_264delGAG) of the CD320 gene. After 5 days of treatment with intravenous vitamin B6 and intramuscular B12-hydroxocobalamine, serum homocysteine was nearly normalized and serum MMA was normalized. At follow-up at 4 months of age, the patient's vitamin B12, homocysteine, and MMA levels were within normal limits. Karth et al. (2012) noted that hyperhomocysteinemia is a known risk factor for retinal vascular occlusive disease; the CRAO in this patient resulted in severe vision loss.

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

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267241.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1East Asian1not providednot providedreference population PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Invitae, SCV000676997.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This variant, c.262_264del, results in the deletion of 1 amino acid(s) of the CD320 protein (p.Glu88del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs150384171, gnomAD 1.4%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individual(s) with methylmalonic aciduria (PMID: 20524213, 22819238, 29663633, 34978764; Invitae). ClinVar contains an entry for this variant (Variation ID: 203643). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CD320 function (PMID: 20524213, 27411955). 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.

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

From Mendelics, SCV001140969.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 2, 2024