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NM_002351.5(SH2D1A):c.1A>G (p.Met1Val) AND X-linked lymphoproliferative disease due to SH2D1A deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 3, 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:
RCV003150604.2

Allele description [Variation Report for NM_002351.5(SH2D1A):c.1A>G (p.Met1Val)]

NM_002351.5(SH2D1A):c.1A>G (p.Met1Val)

Gene:
SH2D1A:SH2 domain containing 1A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq25
Genomic location:
Preferred name:
NM_002351.5(SH2D1A):c.1A>G (p.Met1Val)
HGVS:
  • NC_000023.11:g.124346643A>G
  • NG_007464.1:g.5344A>G
  • NG_033796.2:g.391084A>G
  • NM_001114937.3:c.1A>G
  • NM_002351.5:c.1A>GMANE SELECT
  • NP_001108409.1:p.Met1Val
  • NP_002342.1:p.Met1Val
  • NP_002342.1:p.Met1Val
  • LRG_106t1:c.1A>G
  • LRG_106:g.5344A>G
  • LRG_106p1:p.Met1Val
  • LRG_782:g.391084A>G
  • NC_000023.10:g.123480493A>G
  • NM_002351.4:c.1A>G
Protein change:
M1V
Molecular consequence:
  • NM_001114937.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_002351.5:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001114937.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002351.5:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
X-linked lymphoproliferative disease due to SH2D1A deficiency (XLP1)
Synonyms:
IMMUNODEFICIENCY 5; IMMUNODEFICIENCY, X-LINKED PROGRESSIVE COMBINED VARIABLE; INFECTIOUS MONONUCLEOSIS, SEVERE, SUSCEPTIBILITY TO; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0024551; MedGen: C5399825; Orphanet: 2442; OMIM: 308240

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003837580Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jan 3, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot 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 Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine, SCV003837580.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 1, 2024