NM_000535.7(PMS2):c.325del (p.Glu109fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Nov 2, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000483709.5

Allele description [Variation Report for NM_000535.7(PMS2):c.325del (p.Glu109fs)]

NM_000535.7(PMS2):c.325del (p.Glu109fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.325del (p.Glu109fs)

HGVS:

NC_000007.14:g.6003723del
NG_008466.1:g.10389del
NM_000535.7:c.325delMANE SELECT
NM_001322003.2:c.-81del
NM_001322004.2:c.-81del
NM_001322005.2:c.-81del
NM_001322006.2:c.325del
NM_001322007.2:c.35+254del
NM_001322008.2:c.35+254del
NM_001322009.2:c.-81del
NM_001322010.2:c.-81del
NM_001322011.2:c.-560del
NM_001322012.2:c.-560del
NM_001322013.2:c.-81del
NM_001322014.2:c.325del
NM_001322015.2:c.-160del
NP_000526.2:p.Glu109fs
NP_001308935.1:p.Glu109fs
NP_001308943.1:p.Glu109fs
LRG_161t1:c.325del
LRG_161:g.10389del
NC_000007.13:g.6043349del
NC_000007.13:g.6043354del
NM_000535.5:c.325delG
NM_000535.6:c.325del
NR_136154.1:n.412del
p.E109Kfs*3

Protein change:

E109fs

Links:

dbSNP: rs587781716

NCBI 1000 Genomes Browser:

rs587781716

Molecular consequence:

NM_001322003.2:c.-81del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-81del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-81del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-81del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322010.2:c.-81del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-560del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-560del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-81del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-160del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.325del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.325del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.325del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.35+254del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.35+254del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.412del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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RecName: Full=AP-1 complex subunit beta-1; AltName: Full=Adaptor protein complex...
RecName: Full=AP-1 complex subunit beta-1; AltName: Full=Adaptor protein complex AP-1 subunit beta-1; AltName: Full=Adaptor-related protein complex 1 subunit beta-1; AltName: Full=Beta-1-adaptin; AltName: Full=Beta-adaptin 1; AltName: Full=Clathrin assembly protein complex 1 beta large chain; AltName: Full=Golgi adaptor HA1/AP1 adaptin beta subunit
gi|2203400779|sp|Q10567.3|AP1B1_HUM

Protein
Chain A, CALMODULIN-SENSITIVE ADENYLATE CYCLASE
Chain A, CALMODULIN-SENSITIVE ADENYLATE CYCLASE
gi|18655699|pdb|1K90|A

Protein
BTB/POZ domain-containing protein DOT3-like [Cucurbita maxima]
BTB/POZ domain-containing protein DOT3-like [Cucurbita maxima]
gi|1281002400|ref|XP_022985024.1|

Protein
lysine-specific demethylase JMJ706-like isoform X1 [Benincasa hispida]
lysine-specific demethylase JMJ706-like isoform X1 [Benincasa hispida]
gi|1955861252|ref|XP_038888620.1|

Protein
ER membrane protein complex subunit 7 homolog [Cucumis sativus]
ER membrane protein complex subunit 7 homolog [Cucumis sativus]
gi|1784870679|ref|XP_031739298.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000567847	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Oct 3, 2019)	germline	clinical testing	Citation Link,
SCV003818368	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 2, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000567847

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Oct 3, 2019)

germline

clinical testing

Citation Link,

SCV003818368

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 2, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000567847.4

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek 2016); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Has not been previously published as a pathogenic or benign germline variant to our knowledge; This variant is associated with the following publications: (PMID: 28466842, 28152038)

#	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 Revvity Omics, Revvity, SCV003818368.2

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

#	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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