NM_000535.7(PMS2):c.687T>C (p.Ser229=) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Dec 12, 2018
Review status:: criteria provided, conflicting classifications

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:: RCV000659069.26

Allele description

NM_000535.7(PMS2):c.687T>C (p.Ser229=)

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.687T>C (p.Ser229=)

HGVS:

NC_000007.14:g.5999126A>G
NG_008466.1:g.14981T>C
NM_000535.7:c.687T>CMANE SELECT
NM_001322003.2:c.282T>C
NM_001322004.2:c.282T>C
NM_001322005.2:c.282T>C
NM_001322006.2:c.687T>C
NM_001322007.2:c.369T>C
NM_001322008.2:c.369T>C
NM_001322009.2:c.282T>C
NM_001322010.2:c.282T>C
NM_001322011.2:c.-247T>C
NM_001322012.2:c.-247T>C
NM_001322013.2:c.133-1703T>C
NM_001322014.2:c.687T>C
NM_001322015.2:c.378T>C
NP_000526.2:p.Ser229=
NP_001308932.1:p.Ser94=
NP_001308933.1:p.Ser94=
NP_001308934.1:p.Ser94=
NP_001308935.1:p.Ser229=
NP_001308936.1:p.Ser123=
NP_001308937.1:p.Ser123=
NP_001308938.1:p.Ser94=
NP_001308939.1:p.Ser94=
NP_001308943.1:p.Ser229=
NP_001308944.1:p.Ser126=
LRG_161t1:c.687T>C
LRG_161:g.14981T>C
NC_000007.13:g.6038757A>G
NM_000535.5:c.687T>C
NM_000535.6:c.687T>C
NR_136154.1:n.774T>C
p.S229S

Links:

dbSNP: rs786201508

NCBI 1000 Genomes Browser:

rs786201508

Molecular consequence:

NM_001322011.2:c.-247T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-247T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.133-1703T>C - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.774T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000535.7:c.687T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322003.2:c.282T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322004.2:c.282T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322005.2:c.282T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322006.2:c.687T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322007.2:c.369T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322008.2:c.369T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322009.2:c.282T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322010.2:c.282T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322014.2:c.687T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322015.2:c.378T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens origin recognition complex subunit 4 (ORC4), transcript variant 3, ...
Homo sapiens origin recognition complex subunit 4 (ORC4), transcript variant 3, mRNA
gi|308818132|ref|NM_181742.3|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000729481	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Dec 12, 2018)	germline	clinical testing	Citation Link,
SCV000780878	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Nov 1, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000729481

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Dec 12, 2018)

germline

clinical testing

Citation Link,

SCV000780878

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Nov 1, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000729481.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV000780878.26

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jul 15, 2024

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