NM_000246.3(CIITA):c.931A>G (p.Met311Val) AND Bare lymphocyte syndrome 2

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Oct 23, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000767937.4

Allele description [Variation Report for NM_000246.3(CIITA):c.931A>G (p.Met311Val)]

NM_000246.3(CIITA):c.931A>G (p.Met311Val)

Gene:
CIITA:class II major histocompatibility complex transactivator [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.13
Genomic location:
Preferred name:
NM_000246.3(CIITA):c.931A>G (p.Met311Val)
HGVS:
  • NC_000016.10:g.10903889A>G
  • NG_009628.1:g.31692A>G
  • NM_000246.3:c.931A>G
  • NM_001286402.1:c.934A>G
  • NM_001286403.2:c.784A>G
  • NP_000237.2:p.Met311Val
  • NP_001273331.1:p.Met312Val
  • NP_001273332.1:p.Met262Val
  • LRG_49t1:c.931A>G
  • LRG_49:g.31692A>G
  • LRG_49p1:p.Met311Val
  • NC_000016.9:g.10997746A>G
  • NR_104444.2:n.1060A>G
Protein change:
M262V
Links:
dbSNP: rs140139362
NCBI 1000 Genomes Browser:
rs140139362
Molecular consequence:
  • NM_000246.3:c.931A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286402.1:c.934A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286403.2:c.784A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_104444.2:n.1060A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Bare lymphocyte syndrome 2
Synonyms:
BARE LYMPHOCYTE SYNDROME, TYPE II; BLS, TYPE II; SCID, HLA CLASS II-NEGATIVE; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008855; MedGen: C2931418; Orphanet: 572; OMIM: 209920

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000898612Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicagocriteria provided, single submitter
Uncertain significance
(Dec 3, 2018)
germlineclinical testing

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

SCV001121701Invitaecriteria provided, single submitter
Likely benign
(Oct 23, 2020)
germlineclinical testing

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

SCV001462167Natera, Inc.no assertion criteria providedLikely benign
(Apr 24, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV000898612.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

CIITA NM_000246.3 exon 9 p.Met311Val (c.931A>G): This variant has not been reported in the literature and is present in 0.2% (61/24968) of African alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/16-10997746-A-G). This variant amino acid Valine (Val) is present in several species including multiple primates and other mammals, and it is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

From Invitae, SCV001121701.3

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

From Natera, Inc., SCV001462167.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 6, 2021

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