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NM_000535.7(PMS2):c.1435C>G (p.His479Asp)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 1, 2020
Accession:
VCV000216450.9
Variation ID:
216450
Description:
single nucleotide variant
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NM_000535.7(PMS2):c.1435C>G (p.His479Asp)

Allele ID
212599
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p22.1
Genomic location
7: 5987330 (GRCh38) GRCh38 UCSC
7: 6026961 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_161:g.26777C>G
LRG_161t1:c.1435C>G
NC_000007.13:g.6026961G>C
... more HGVS
Protein change
H479D, H344D, H373D, H376D, H427D, H168D, H288D, H292D
Other names
-
Canonical SPDI
NC_000007.14:5987329:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA043547
dbSNP: rs376344586
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 3 criteria provided, multiple submitters, no conflicts Jul 6, 2020 RCV000216807.5
Uncertain significance 1 criteria provided, single submitter Nov 1, 2020 RCV000197213.4
Uncertain significance 1 criteria provided, single submitter Jan 20, 2017 RCV000487350.1
Uncertain significance 1 criteria provided, single submitter May 2, 2019 RCV001192581.1
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV001160657.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PMS2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
3086 3151

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 20, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000569889.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This variant is denoted PMS2 c.1435C>G at the cDNA level, p.His479Asp (H479D) at the protein level, and results in the change of a Histidine to … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal cancer type 4
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001322474.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 17, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000903881.2
Submitted: (May 19, 2020)
Evidence details
Uncertain significance
(May 02, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001360810.1
Submitted: (Mar 06, 2020)
Evidence details
Comment:
Variant summary: PMS2 c.1435C>G (p.His479Asp) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign … (more)
Uncertain significance
(Jul 06, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000277878.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
The p.H479D variant (also known as c.1435C>G), located in coding exon 11 of the PMS2 gene, results from a C to G substitution at nucleotide … (more)
Uncertain significance
(Nov 01, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary nonpolyposis colorectal neoplasms
Allele origin: germline
Invitae
Accession: SCV000254598.5
Submitted: (Jan 07, 2021)
Evidence details
Comment:
This sequence change replaces histidine with aspartic acid at codon 479 of the PMS2 protein (p.His479Asp). The histidine residue is weakly conserved and there is … (more)
Likely benign
(May 09, 2018)
no assertion criteria provided
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
True Health Diagnostics
Accession: SCV000805282.1
Submitted: (Jun 26, 2018)
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 rs376344586...

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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 Nov 27, 2021