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NM_004048.4(B2M):c.154_155delinsTT (p.Pro52Leu) AND Hypoproteinemia, hypercatabolic

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 20, 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:
RCV001871910.4

Allele description [Variation Report for NM_004048.4(B2M):c.154_155delinsTT (p.Pro52Leu)]

NM_004048.4(B2M):c.154_155delinsTT (p.Pro52Leu)

Gene:
B2M:beta-2-microglobulin [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
15q21.1
Genomic location:
Preferred name:
NM_004048.4(B2M):c.154_155delinsTT (p.Pro52Leu)
Other names:
B2M, PRO52LEU
HGVS:
  • NC_000015.10:g.44715509_44715510delinsTT
  • NG_012920.2:g.9033_9034delinsTT
  • NM_004048.4:c.154_155delinsTTMANE SELECT
  • NP_004039.1:p.Pro52Leu
  • NP_004039.1:p.Pro52Leu
  • LRG_1215t1:c.154_155delinsTT
  • LRG_1215:g.9033_9034delinsTT
  • NC_000015.9:g.45007707_45007708delinsTT
  • NM_004048.3:c.154_155delCCinsTT
  • NM_004048.3:c.154_155delinsTT
Protein change:
P52L; PRO52LEU
Links:
OMIM: 109700.0004; dbSNP: rs2141288680
NCBI 1000 Genomes Browser:
rs2141288680
Molecular consequence:
  • NM_004048.4:c.154_155delinsTT - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hypoproteinemia, hypercatabolic (IMD43)
Synonyms:
IMMUNODEFICIENCY 43; BETA-2-MICROGLOBULIN DEFICIENCY; B2M DEFICIENCY; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009434; MedGen: C1855796; OMIM: 241600

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002239859Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 20, 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV002239859.2

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

Description

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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals with B2M-related conditions. The frequency data for this variant in the population databases is not available, as this variant may be reported as separate entries in the ExAC database. This sequence change replaces proline with leucine at codon 52 of the B2M protein (p.Pro52Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine.

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

Last Updated: May 26, 2024