NM_000535.7(PMS2):c.1415A>G (p.Lys472Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 7, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV004066666.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1415A>G (p.Lys472Arg)]

NM_000535.7(PMS2):c.1415A>G (p.Lys472Arg)

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.1415A>G (p.Lys472Arg)

HGVS:

NC_000007.14:g.5987350T>C
NG_008466.1:g.26757A>G
NM_000535.7:c.1415A>GMANE SELECT
NM_001018040.1:c.1010A>G
NM_001322003.2:c.1010A>G
NM_001322004.2:c.1010A>G
NM_001322005.2:c.1010A>G
NM_001322006.2:c.1259A>G
NM_001322007.2:c.1097A>G
NM_001322008.2:c.1097A>G
NM_001322009.2:c.1010A>G
NM_001322010.2:c.854A>G
NM_001322011.2:c.482A>G
NM_001322012.2:c.482A>G
NM_001322013.2:c.842A>G
NM_001322014.2:c.1415A>G
NM_001322015.2:c.1106A>G
NM_001406866.1:c.1601A>G
NM_001406868.1:c.1439A>G
NM_001406869.1:c.1307A>G
NM_001406870.1:c.1259A>G
NM_001406871.1:c.1415A>G
NM_001406872.1:c.1415A>G
NM_001406873.1:c.1217A>G
NM_001406874.1:c.1247A>G
NM_001406875.1:c.1106A>G
NM_001406876.1:c.1097A>G
NM_001406877.1:c.1106A>G
NM_001406878.1:c.1106A>G
NM_001406879.1:c.1106A>G
NM_001406880.1:c.1106A>G
NM_001406881.1:c.1106A>G
NM_001406882.1:c.1106A>G
NM_001406883.1:c.1097A>G
NM_001406884.1:c.1091A>G
NM_001406885.1:c.1079A>G
NM_001406886.1:c.1049A>G
NM_001406887.1:c.1010A>G
NM_001406888.1:c.1010A>G
NM_001406889.1:c.1010A>G
NM_001406890.1:c.1010A>G
NM_001406891.1:c.1010A>G
NM_001406892.1:c.1010A>G
NM_001406893.1:c.1010A>G
NM_001406894.1:c.1010A>G
NM_001406895.1:c.1010A>G
NM_001406896.1:c.1010A>G
NM_001406897.1:c.1010A>G
NM_001406898.1:c.1010A>G
NM_001406899.1:c.1010A>G
NM_001406900.1:c.950A>G
NM_001406901.1:c.941A>G
NM_001406902.1:c.941A>G
NM_001406903.1:c.1097A>G
NM_001406904.1:c.902A>G
NM_001406905.1:c.902A>G
NM_001406906.1:c.854A>G
NM_001406907.1:c.854A>G
NM_001406908.1:c.1010A>G
NM_001406909.1:c.842A>G
NM_001406910.1:c.1010A>G
NM_001406911.1:c.644A>G
NP_000526.1:p.Lys472Arg
NP_000526.2:p.Lys472Arg
NP_001018050.1:p.Lys337Arg
NP_001308932.1:p.Lys337Arg
NP_001308933.1:p.Lys337Arg
NP_001308934.1:p.Lys337Arg
NP_001308935.1:p.Lys420Arg
NP_001308936.1:p.Lys366Arg
NP_001308937.1:p.Lys366Arg
NP_001308938.1:p.Lys337Arg
NP_001308939.1:p.Lys285Arg
NP_001308940.1:p.Lys161Arg
NP_001308941.1:p.Lys161Arg
NP_001308942.1:p.Lys281Arg
NP_001308943.1:p.Lys472Arg
NP_001308944.1:p.Lys369Arg
NP_001393795.1:p.Lys534Arg
NP_001393797.1:p.Lys480Arg
NP_001393798.1:p.Lys436Arg
NP_001393799.1:p.Lys420Arg
NP_001393800.1:p.Lys472Arg
NP_001393801.1:p.Lys472Arg
NP_001393802.1:p.Lys406Arg
NP_001393803.1:p.Lys416Arg
NP_001393804.1:p.Lys369Arg
NP_001393805.1:p.Lys366Arg
NP_001393806.1:p.Lys369Arg
NP_001393807.1:p.Lys369Arg
NP_001393808.1:p.Lys369Arg
NP_001393809.1:p.Lys369Arg
NP_001393810.1:p.Lys369Arg
NP_001393811.1:p.Lys369Arg
NP_001393812.1:p.Lys366Arg
NP_001393813.1:p.Lys364Arg
NP_001393814.1:p.Lys360Arg
NP_001393815.1:p.Lys350Arg
NP_001393816.1:p.Lys337Arg
NP_001393817.1:p.Lys337Arg
NP_001393818.1:p.Lys337Arg
NP_001393819.1:p.Lys337Arg
NP_001393820.1:p.Lys337Arg
NP_001393821.1:p.Lys337Arg
NP_001393822.1:p.Lys337Arg
NP_001393823.1:p.Lys337Arg
NP_001393824.1:p.Lys337Arg
NP_001393825.1:p.Lys337Arg
NP_001393826.1:p.Lys337Arg
NP_001393827.1:p.Lys337Arg
NP_001393828.1:p.Lys337Arg
NP_001393829.1:p.Lys317Arg
NP_001393830.1:p.Lys314Arg
NP_001393831.1:p.Lys314Arg
NP_001393832.1:p.Lys366Arg
NP_001393833.1:p.Lys301Arg
NP_001393834.1:p.Lys301Arg
NP_001393835.1:p.Lys285Arg
NP_001393836.1:p.Lys285Arg
NP_001393837.1:p.Lys337Arg
NP_001393838.1:p.Lys281Arg
NP_001393839.1:p.Lys337Arg
NP_001393840.1:p.Lys215Arg
LRG_161t1:c.1415A>G
LRG_161:g.26757A>G
LRG_161p1:p.Lys472Arg
NC_000007.13:g.6026981T>C
NM_000535.5:c.1415A>G
NR_003085.2:n.1497A>G
NR_136154.1:n.1502A>G

Protein change:

K161R

Molecular consequence:

NM_000535.7:c.1415A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001018040.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.1259A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.1097A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.1097A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.854A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.482A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.482A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.842A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.1415A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406866.1:c.1601A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406868.1:c.1439A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406869.1:c.1307A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406870.1:c.1259A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406871.1:c.1415A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406872.1:c.1415A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406873.1:c.1217A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406874.1:c.1247A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406875.1:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406876.1:c.1097A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406877.1:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406878.1:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406879.1:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406880.1:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406881.1:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406882.1:c.1106A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406883.1:c.1097A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406884.1:c.1091A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406885.1:c.1079A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406886.1:c.1049A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406887.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406888.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406889.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406890.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406891.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406892.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406893.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406894.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406895.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406896.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406897.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406898.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406899.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406900.1:c.950A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406901.1:c.941A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406902.1:c.941A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406903.1:c.1097A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406904.1:c.902A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406905.1:c.902A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406906.1:c.854A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406907.1:c.854A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406908.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406909.1:c.842A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406910.1:c.1010A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406911.1:c.644A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.1502A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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Mus musculus RAB7B, member RAS oncogene family (Rab7b), transcript variant 1, mR...
Mus musculus RAB7B, member RAS oncogene family (Rab7b), transcript variant 1, mRNA
gi|902763209|ref|NM_145509.3|

Nucleotide
collagen alpha-1(XXIV) chain isoform X4 [Homo sapiens]
collagen alpha-1(XXIV) chain isoform X4 [Homo sapiens]
gi|2462507496|ref|XP_054191766.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005035993	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Mar 7, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005035993

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Mar 7, 2024)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV005035993.1

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

Description

The p.K472R variant (also known as c.1415A>G), located in coding exon 11 of the PMS2 gene, results from an A to G substitution at nucleotide position 1415. The lysine at codon 472 is replaced by arginine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, the clinical significance of this alteration remains unclear.

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

Last Updated: Sep 29, 2024

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