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NM_000074.3(CD40LG):c.770G>T (p.Gly257Val) AND Hyper-IgM syndrome type 1

Germline classification:
Likely pathogenic (1 submission)
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:
RCV003228759.1

Allele description [Variation Report for NM_000074.3(CD40LG):c.770G>T (p.Gly257Val)]

NM_000074.3(CD40LG):c.770G>T (p.Gly257Val)

Gene:
CD40LG:CD40 ligand [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq26.3
Genomic location:
Preferred name:
NM_000074.3(CD40LG):c.770G>T (p.Gly257Val)
HGVS:
  • NC_000023.11:g.136659399G>T
  • NG_007280.1:g.16223G>T
  • NM_000074.3:c.770G>TMANE SELECT
  • NP_000065.1:p.Gly257Val
  • NP_000065.1:p.Gly257Val
  • LRG_141t1:c.770G>T
  • LRG_141:g.16223G>T
  • LRG_141p1:p.Gly257Val
  • NC_000023.10:g.135741558G>T
  • NM_000074.2:c.770G>T
Protein change:
G257V
Molecular consequence:
  • NM_000074.3:c.770G>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Hyper-IgM syndrome type 1
Synonyms:
Immunodeficiency with hyper IgM type 1; Hyper IgM immunodeficiency, X-linked; Hyper-IgM Immunodeficiency Syndrome, Type 1; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010626; MedGen: C0398689; OMIM: 308230

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003925474Lifecell International Pvt. Ltd
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Asiangermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Lifecell International Pvt. Ltd, SCV003925474.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Asian1not providednot providedclinical testing PubMed (1)

Description

A Hemizygote Missense variant c.770G>T in Exon 5 of the CD40LG gene that results in the amino acid substitution p.Gly257Val was identified. The observed variant has a minimum allele frequency of 00/00% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. Based on the above evidence this variant has been classified as Likely Pathogenic according to the ACMG guidelines.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Apr 6, 2024