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

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Interpretation:
Conflicting interpretations of pathogenicity, other​

Likely benign(1);Likely pathogenic(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 20, 2020
Accession:
VCV000203643.6
Variation ID:
203643
Description:
3bp microsatellite
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NM_016579.4(CD320):c.256GAG[2] (p.Glu88del)

Allele ID
200359
Variant type
Microsatellite
Variant length
3 bp
Cytogenetic location
19p13.2
Genomic location
19: 8305035-8305037 (GRCh38) GRCh38 UCSC
19: 8369919-8369921 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NG_028124.1:g.8314GAG[2]
NC_000019.9:g.8369919CTC[2]
NC_000019.10:g.8305035CTC[2]
... more HGVS
Protein change
E88del
Other names
-
Canonical SPDI
NC_000019.10:8305034:CTCCTCCTC:CTCCTC
Functional consequence
-
Global minor allele frequency (GMAF)
0.00699 (CTCCTC)

Allele frequency
-
Links
dbSNP: rs150384171
ClinGen: CA312377
OMIM: 606475.0001
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign, other 2 criteria provided, multiple submitters, no conflicts Mar 15, 2017 RCV000224888.3
Uncertain significance 1 criteria provided, single submitter Jan 16, 2017 RCV000185812.3
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Oct 20, 2020 RCV000004499.10
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CD320 - - GRCh38
GRCh37
82 93

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Mar 18, 2016)
criteria provided, single submitter
Method: reference population
Methylmalonic aciduria due to transcobalamin receptor defect
Allele origin: germline
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center
Accession: SCV000267241.1
Submitted: (Apr 14, 2016)
Evidence details
Publications
PubMed (1)
Likely Benign
(Feb 02, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000280766.1
Submitted: (May 19, 2016)
Evidence details
Comment:
Converted during submission to Likely benign.
Uncertain significance
(Jan 16, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000238758.11
Submitted: (Nov 28, 2017)
Evidence details
Comment:
The c.262_264delGAG variant has been published as a pathogenic variant in association with transcobalamin II receptor defect in a patient with an abnormal newborn screening … (more)
other
(Mar 15, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000700738.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Methylmalonic aciduria due to transcobalamin receptor defect
Allele origin: unknown
Mendelics
Accession: SCV001140969.1
Submitted: (Oct 22, 2019)
Evidence details
Uncertain significance
(Oct 20, 2020)
criteria provided, single submitter
Method: clinical testing
Methylmalonic aciduria due to transcobalamin receptor defect
Allele origin: germline
Invitae
Accession: SCV000676997.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This variant, c.262_264delGAG, results in the deletion of 1 amino acid of the CD320 protein (p.Glu88del), but otherwise preserves the integrity of the reading frame. … (more)
Pathogenic
(Aug 01, 2010)
no assertion criteria provided
Method: literature only
METHYLMALONIC ACIDURIA, TRANSIENT, DUE TO TRANSCOBALAMIN RECEPTOR DEFECT
Allele origin: germline
OMIM
Accession: SCV000024673.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Transcobalamin receptor defect: Identification of two new cases through positive newborn screening for propionic/methylmalonic aciduria and long-term outcome. Hannah-Shmouni F American journal of medical genetics. Part A 2018 PMID: 29663633
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Kobayashi Y Genome medicine 2017 PMID: 28166811
Structural basis of transcobalamin recognition by human CD320 receptor. Alam A Nature communications 2016 PMID: 27411955
Bilateral central retinal artery occlusions in an infant with hyperhomocysteinemia. Karth P Journal of AAPOS : the official publication of the American Association for Pediatric Ophthalmology and Strabismus 2012 PMID: 22819238
Positive newborn screen for methylmalonic aciduria identifies the first mutation in TCblR/CD320, the gene for cellular uptake of transcobalamin-bound vitamin B(12). Quadros EV Human mutation 2010 PMID: 20524213
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CD320 - - - -

Text-mined citations for rs150384171...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 14, 2021