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NM_000433.3(NCF2):c.1081A>T (p.Thr361Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 1, 2021)
Last evaluated:
Jun 1, 2021
Accession:
VCV000466297.8
Variation ID:
466297
Description:
single nucleotide variant
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NM_000433.3(NCF2):c.1081A>T (p.Thr361Ser)

Allele ID
447538
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q25.3
Genomic location
1: 183563531 (GRCh38) GRCh38 UCSC
1: 183532666 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_88t1:c.1081A>T LRG_88p1:p.Thr361Ser
LRG_88:g.32051A>T
NC_000001.10:g.183532666T>A
... more HGVS
Protein change
T361S, T316S, T280S
Other names
-
Canonical SPDI
NC_000001.11:183563530:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00240 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00179
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00200
1000 Genomes Project 0.00240
The Genome Aggregation Database (gnomAD) 0.00108
Exome Aggregation Consortium (ExAC) 0.00187
The Genome Aggregation Database (gnomAD), exomes 0.00192
Links
ClinGen: CA1284684
dbSNP: rs147744729
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, single submitter Jun 1, 2021 RCV001532089.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 3, 2020 RCV000526618.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NCF2 - - GRCh38
GRCh37
234 260

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2
Allele origin: germline
Invitae
Accession: SCV000641903.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(May 25, 2017)
criteria provided, single submitter
Method: clinical testing
Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001257653.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(May 21, 2020)
criteria provided, single submitter
Method: clinical testing
Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2
Allele origin: germline
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
Accession: SCV001468386.1
Submitted: (Dec 29, 2020)
Evidence details
Comment:
NCF2 NM_000433.3 exon 12 p.Thr361Ser (c.1081A>T): This variant has been reported in the literature in at least one individual with inflammatory bowel disease (Denson 2018 … (more)
Uncertain significance
(Jun 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001747486.1
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(Dec 07, 2020)
no assertion criteria provided
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001820040.1
Submitted: (Sep 01, 2021)
Evidence details
Comment:
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29454792)

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 rs147744729...

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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 Sep 07, 2021