NM_001250.6(CD40):c.832_*1del (p.Ter278AlaextTer?) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 24, 2023
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:: RCV003064608.4

Allele description [Variation Report for NM_001250.6(CD40):c.832_*1del (p.Ter278AlaextTer?)]

NM_001250.6(CD40):c.832_*1del (p.Ter278AlaextTer?)

Gene:

CD40:CD40 molecule [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

20q13.12

Genomic location:

Preferred name:

NM_001250.6(CD40):c.832_*1del (p.Ter278AlaextTer?)

HGVS:

NC_000020.11:g.46129038_46129041del
NG_007279.1:g.15772_15775del
NM_001250.6:c.832_*1delMANE SELECT
NM_001302753.2:c.*158_*161del
NM_001322421.2:c.844_*1del
NM_001322422.2:c.676_*1del
NM_001362758.2:c.*158_*161del
NM_152854.4:c.*158_*161del
NP_001241.1:p.Ter278AlaextTer?
NP_001241.1:p.Ter278_Ter(278_?)(?)
NP_001309350.1:p.Ter282AlaextTer?
NP_001309351.1:p.Ter226AlaextTer?
LRG_40t1:c.832_*1del
LRG_40:g.15772_15775del
LRG_40p1:p.Ter278_Ter(278_?)(?)
NC_000020.10:g.44757675_44757678del
NC_000020.10:g.44757677_44757680del
NM_001250.4:c.832_*1delTGAG
NR_126502.2:n.865_868del
NR_136327.2:n.768_771del

Molecular consequence:

NM_001302753.2:c.*158_*161del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001362758.2:c.*158_*161del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152854.4:c.*158_*161del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001250.6:c.832_*1del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322421.2:c.844_*1del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322422.2:c.676_*1del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_126502.2:n.865_868del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_136327.2:n.768_771del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001250.6:c.832_*1del - stop lost - [Sequence Ontology: SO:0001578]
NM_001322421.2:c.844_*1del - stop lost - [Sequence Ontology: SO:0001578]
NM_001322422.2:c.676_*1del - stop lost - [Sequence Ontology: SO:0001578]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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PODANS_5_1200 [Podospora anserina S mat+]
PODANS_5_1200 [Podospora anserina S mat+]
Gene ID:6188456

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003443838	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Apr 24, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22443339, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003443838

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Apr 24, 2023)

germline

clinical testing

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

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

Hyper-immunoglobulin M syndrome type 3 with normal CD40 cell surface expression.

Karaca NE, Forveille M, Aksu G, Durandy A, Kutukculer N.

Scand J Immunol. 2012 Jul;76(1):21-5. doi: 10.1111/j.1365-3083.2012.02697.x.

PubMed [citation]

PMID:: 22443339

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, SCV003443838.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. ClinVar contains an entry for this variant (Variation ID: 2138351). This variant is also known as c.831‚Äì834 delTAGG p.X277ins33. This protein extension has been observed in individuals with clinical features of autosomal recessive hyper IgM syndrome (PMID: 22443339; Invitae). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change disrupts the translational stop signal of the CD40 mRNA. It is expected to extend the length of the CD40 protein by 33 additional amino acid residues.

#	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

ClinVar

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