U.S. flag

An official website of the United States government

NM_001363118.2(SLC52A2):c.402CTT[1] (p.Phe135del) AND Brown-Vialetto-van Laere syndrome 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 7, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001269384.2

Allele description [Variation Report for NM_001363118.2(SLC52A2):c.402CTT[1] (p.Phe135del)]

NM_001363118.2(SLC52A2):c.402CTT[1] (p.Phe135del)

Gene:
SLC52A2:solute carrier family 52 member 2 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
8q24.3
Genomic location:
Preferred name:
NM_001363118.2(SLC52A2):c.402CTT[1] (p.Phe135del)
HGVS:
  • NC_000008.11:g.144359894CTT[1]
  • NG_032872.2:g.6338CTT[1]
  • NM_001253815.2:c.402CTT[1]
  • NM_001253816.2:c.402CTT[1]
  • NM_001363118.2:c.402CTT[1]MANE SELECT
  • NM_001363120.2:c.402CTT[1]
  • NM_001363121.2:c.402CTT[1]
  • NM_001363122.2:c.131-218_131-216del
  • NM_024531.5:c.402CTT[1]
  • NP_001240744.1:p.Phe135del
  • NP_001240745.1:p.Phe135del
  • NP_001350047.1:p.Phe135del
  • NP_001350049.1:p.Phe135del
  • NP_001350050.1:p.Phe135del
  • NP_078807.1:p.Phe135del
  • NC_000008.10:g.145583554CTT[1]
  • NG_032872.1:g.6338CTT[1]
  • NM_024531.4:c.405_407delCTT
  • NR_045600.2:n.862CTT[1]
Protein change:
F135del
Links:
dbSNP: rs1337709383
NCBI 1000 Genomes Browser:
rs1337709383
Molecular consequence:
  • NM_001253815.2:c.402CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001253816.2:c.402CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001363118.2:c.402CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001363120.2:c.402CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001363121.2:c.402CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_024531.5:c.402CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001363122.2:c.131-218_131-216del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_045600.2:n.862CTT[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Functional consequence:
Decreased function
Observations:
1

Condition(s)

Name:
Brown-Vialetto-van Laere syndrome 2
Synonyms:
Riboflavin transporter deficiency type 2
Identifiers:
MONDO: MONDO:0013867; MedGen: C3553538; Orphanet: 97229; OMIM: 614707

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001335263Elsea Laboratory, Baylor College of Medicine
no assertion criteria provided
Pathogenic
(Jun 7, 2020) 		germline, not applicableclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providednot applicablenot applicablenot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Elsea Laboratory, Baylor College of Medicine, SCV001335263.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testingnot provided
2not providednot providednot providednot providedclinical testingnot provided

Description

Patient has clinical features of riboflavin transporter deficiency and treatment improved symptoms. He has a known pathogenic variant detected by WES in addition to this variant. Acylcarnitine analysis and untargeted metabolomics detected biochemical changes confirming the diagnosis. The c.405_407delCTT variant has not been previously described as a pathogenic variant or a benign variant to our knowledge. This variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). In silico analyses, including splice predictors, further supports a deleterious effect.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided
2not applicablenot applicablenot providedplasmanot providednot providednot providednot providednot provided

Last Updated: Aug 26, 2023