NM_001195263.2(PDZD7):c.2368A>G (p.Lys790Glu) AND not provided

Germline classification:: Benign (4 submissions)
Last evaluated:: Jan 31, 2024
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:: RCV000712520.11

Allele description [Variation Report for NM_001195263.2(PDZD7):c.2368A>G (p.Lys790Glu)]

NM_001195263.2(PDZD7):c.2368A>G (p.Lys790Glu)

Gene:

PDZD7:PDZ domain containing 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q24.31

Genomic location:

Preferred name:

NM_001195263.2(PDZD7):c.2368A>G (p.Lys790Glu)

HGVS:

NC_000010.11:g.101010521T>C
NG_028030.1:g.25637A>G
NM_001195263.2:c.2368A>GMANE SELECT
NP_001182192.1:p.Lys790Glu
NC_000010.10:g.102770278T>C
NM_001195263.1:c.2368A>G
c.2368A>G

Protein change:

K790E

Links:

dbSNP: rs111287837

NCBI 1000 Genomes Browser:

rs111287837

Molecular consequence:

NM_001195263.2:c.2368A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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phosphatidylinositol 3-kinase regulatory subunit gamma isoform 3 [Rattus norvegi...
phosphatidylinositol 3-kinase regulatory subunit gamma isoform 3 [Rattus norvegicus]
gi|2725385622|ref|NP_001416851.1|

Protein
PREDICTED: Momordica charantia pectin acetylesterase 8-like (LOC111008290), tran...
PREDICTED: Momordica charantia pectin acetylesterase 8-like (LOC111008290), transcript variant X1, mRNA
gi|1229767655|ref|XM_022280937.1|

Nucleotide
PREDICTED: Mus musculus COP9 signalosome subunit 3 (Cops3), transcript variant X...
PREDICTED: Mus musculus COP9 signalosome subunit 3 (Cops3), transcript variant X1, mRNA
gi|1720366159|ref|XM_030246025.1|

Nucleotide
PREDICTED: Cucurbita moschata stress-response A/B barrel domain-containing prote...
PREDICTED: Cucurbita moschata stress-response A/B barrel domain-containing protein UP3 (LOC111437663), transcript variant X1, mRNA
gi|1279841925|ref|XM_023075741.1|

Nucleotide
Sar 28S ribosomal RNA gene, partial sequence.
Sar 28S ribosomal RNA gene, partial sequence.
PopSet: 1028341418

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000843025	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (May 24, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000970143	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jun 2, 2018)	germline	clinical testing	Citation Link,
SCV001728617	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005320071	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

See all PubMed Citations (3)

Details of each submission

From Athena Diagnostics, SCV000843025.1

#	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

From GeneDx, SCV000970143.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001728617.4

#	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

From Breakthrough Genomics, Breakthrough Genomics, SCV005320071.1

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

#	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

Last Updated: Sep 29, 2024

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