NM_000626.4(CD79B):c.467C>T (p.Thr156Met) AND Agammaglobulinemia 6, autosomal recessive

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 25, 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:: RCV002018386.5

Allele description [Variation Report for NM_000626.4(CD79B):c.467C>T (p.Thr156Met)]

NM_000626.4(CD79B):c.467C>T (p.Thr156Met)

Genes:

CD79B:CD79b molecule [Gene - OMIM - HGNC]
GH-LCR:growth hormone locus control region [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

17q23.3

Genomic location:

Preferred name:

NM_000626.4(CD79B):c.467C>T (p.Thr156Met)

HGVS:

NC_000017.11:g.63929852G>A
NG_007368.1:g.7493C>T
NG_042788.1:g.12760G>A
NM_000626.4:c.467C>TMANE SELECT
NM_001039933.3:c.470C>T
NM_001329050.2:c.158C>T
NM_021602.4:c.155C>T
NP_000617.1:p.Thr156Met
NP_001035022.1:p.Thr157Met
NP_001315979.1:p.Thr53Met
NP_067613.1:p.Thr52Met
LRG_43:g.7493C>T
NC_000017.10:g.62007212G>A

Protein change:

T156M

Links:

dbSNP: rs2144756917

NCBI 1000 Genomes Browser:

rs2144756917

Molecular consequence:

NM_000626.4:c.467C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001039933.3:c.470C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001329050.2:c.158C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_021602.4:c.155C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Agammaglobulinemia 6, autosomal recessive (AGM6)
Synonyms:: AGAMMAGLOBULINEMIA 6; AGAMMAGLOBULINEMIA, AUTOSOMAL RECESSIVE, DUE TO CD79B DEFECT
Identifiers:: MONDO: MONDO:0012987; MedGen: C3150207; OMIM: 612692

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002299858	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 25, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002299858

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 25, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002299858.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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 output the following: SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available". The methionine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with CD79B-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with methionine at codon 156 of the CD79B protein (p.Thr156Met). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and methionine.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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