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NM_001250.6(CD40):c.408A>T (p.Thr136=) AND Hyper-IgM syndrome type 3

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 23, 2001
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:
RCV000019324.28

Allele description [Variation Report for NM_001250.6(CD40):c.408A>T (p.Thr136=)]

NM_001250.6(CD40):c.408A>T (p.Thr136=)

Gene:
CD40:CD40 molecule [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q13.12
Genomic location:
Preferred name:
NM_001250.6(CD40):c.408A>T (p.Thr136=)
Other names:
CD40, 455A-T, +5, EX5
HGVS:
  • NC_000020.11:g.46123130A>T
  • NG_007279.1:g.9864A>T
  • NM_001250.6:c.408A>TMANE SELECT
  • NM_001302753.2:c.408A>T
  • NM_001322421.2:c.408A>T
  • NM_001322422.2:c.403+374A>T
  • NM_001362758.2:c.408A>T
  • NM_152854.4:c.408A>T
  • NP_001241.1:p.Thr136=
  • NP_001289682.1:p.Thr136=
  • NP_001309350.1:p.Thr136=
  • NP_001349687.1:p.Thr136=
  • NP_690593.1:p.Thr136=
  • LRG_40:g.9864A>T
  • NC_000020.10:g.44751769A>T
Links:
OMIM: 109535.0001; dbSNP: rs2145595063
NCBI 1000 Genomes Browser:
rs2145595063
Molecular consequence:
  • NM_001322422.2:c.403+374A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001250.6:c.408A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001302753.2:c.408A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322421.2:c.408A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001362758.2:c.408A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_152854.4:c.408A>T - synonymous variant - [Sequence Ontology: SO:0001819]
Functional consequence:
exon loss [Variation Ontology: 0381]

Condition(s)

Name:
Hyper-IgM syndrome type 3
Synonyms:
Immunodeficiency with hyper IgM type 3; Hyper-IgM Immunodeficiency Syndrome, Type 3
Identifiers:
MONDO: MONDO:0011735; MedGen: C1720957; OMIM: 606843

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000039614OMIM
no assertion criteria provided
Pathogenic
(Oct 23, 2001) 		germlineliterature only

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutations of CD40 gene cause an autosomal recessive form of immunodeficiency with hyper IgM.

Ferrari S, Giliani S, Insalaco A, Al-Ghonaium A, Soresina AR, Loubser M, Avanzini MA, Marconi M, Badolato R, Ugazio AG, Levy Y, Catalan N, Durandy A, Tbakhi A, Notarangelo LD, Plebani A.

Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12614-9.

PubMed [citation]
PMID:
11675497
PMCID:
PMC60102

Details of each submission

From OMIM, SCV000039614.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In an 8-year-old Italian female with immunodeficiency with hyper-IgM (HIGM3; 606843), born of consanguineous parents, Ferrari et al. (2001) found homozygosity for a silent mutation, a 455A-T transversion, at the fifth basepair position of exon 5 of the CD40 gene, involving an exonic splicing enhancer and leading to exon skipping and premature termination. Flow cytometric analysis of patient lymphoblastoid cells showed lack of surface CD40 expression. Glycosylation studies and confocal microscopy showed that the mutant protein was retained in the endoplasmic reticulum.

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

Last Updated: Dec 24, 2023