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

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 23, 2020
Accession:
VCV000625921.5
Variation ID:
625921
Description:
single nucleotide variant
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NM_000246.3(CIITA):c.931A>G (p.Met311Val)

Allele ID
614409
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.13
Genomic location
16: 10903889 (GRCh38) GRCh38 UCSC
16: 10997746 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.10903889A>G
NC_000016.9:g.10997746A>G
NM_001286402.1:c.934A>G NP_001273331.1:p.Met312Val missense
... more HGVS
Protein change
M311V, M262V, M312V
Other names
-
Canonical SPDI
NC_000016.10:10903888:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (G)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00017
Exome Aggregation Consortium (ExAC) 0.00016
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00043
The Genome Aggregation Database (gnomAD) 0.00061
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
Links
dbSNP: rs140139362
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Oct 23, 2020 RCV000767937.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CIITA - - GRCh38
GRCh37
736 763

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 03, 2018)
criteria provided, single submitter
Method: clinical testing
Bare lymphocyte syndrome 2
Allele origin: germline
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
Accession: SCV000898612.1
Submitted: (Dec 12, 2018)
Evidence details
Comment:
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 … (more)
Likely benign
(Oct 23, 2020)
criteria provided, single submitter
Method: clinical testing
Bare lymphocyte syndrome 2
Allele origin: germline
Invitae
Accession: SCV001121701.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Apr 24, 2020)
no assertion criteria provided
Method: clinical testing
Bare lymphocyte syndrome type II
Allele origin: germline
Natera, Inc.
Accession: SCV001462167.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs140139362...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 06, 2021