NM_001242896.3(DEPDC5):c.3311C>T (p.Ser1104Leu) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Apr 7, 2022
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:: RCV001668361.12

Allele description [Variation Report for NM_001242896.3(DEPDC5):c.3311C>T (p.Ser1104Leu)]

NM_001242896.3(DEPDC5):c.3311C>T (p.Ser1104Leu)

Gene:

DEPDC5:DEP domain containing 5, GATOR1 subcomplex subunit [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.3

Genomic location:

Preferred name:

NM_001242896.3(DEPDC5):c.3311C>T (p.Ser1104Leu)

HGVS:

NC_000022.11:g.31861414C>T
NG_034067.1:g.112464C>T
NM_001136029.4:c.3284C>T
NM_001242896.3:c.3311C>TMANE SELECT
NM_001242897.2:c.3030+3861C>T
NM_001363852.2:c.3264+3861C>T
NM_001363854.2:c.3077C>T
NM_001364318.2:c.3311C>T
NM_001364319.2:c.3077C>T
NM_001364320.2:c.3264+3861C>T
NM_001369901.1:c.3227C>T
NM_001369902.1:c.3227C>T
NM_001369903.1:c.3237+3861C>T
NM_014662.6:c.3237+3861C>T
NP_001129501.1:p.Ser1095Leu
NP_001229825.1:p.Ser1104Leu
NP_001229825.1:p.Ser1104Leu
NP_001350783.1:p.Ser1026Leu
NP_001351247.1:p.Ser1104Leu
NP_001351248.1:p.Ser1026Leu
NP_001356830.1:p.Ser1076Leu
NP_001356831.1:p.Ser1076Leu
NC_000022.10:g.32257400C>T
NM_001242896.1:c.3311C>T
NR_146296.2:n.3400C>T
NR_157126.2:n.3400C>T
O75140:p.Ser1104Leu

Protein change:

S1026L

Links:

UniProtKB: O75140#VAR_069266; dbSNP: rs79027628

NCBI 1000 Genomes Browser:

rs79027628

Molecular consequence:

NM_001242897.2:c.3030+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001363852.2:c.3264+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001364320.2:c.3264+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001369903.1:c.3237+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_014662.6:c.3237+3861C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001136029.4:c.3284C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242896.3:c.3311C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363854.2:c.3077C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364318.2:c.3311C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001364319.2:c.3077C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369901.1:c.3227C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369902.1:c.3227C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_146296.2:n.3400C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_157126.2:n.3400C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001889294	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Jun 25, 2020)	germline	clinical testing	Citation Link,
SCV003834327	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 7, 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

SCV001889294

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Jun 25, 2020)

germline

clinical testing

Citation Link,

SCV003834327

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 7, 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, SCV001889294.1

#	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 associated with the following publications: (PMID: 31639411, 31594065, 31139143, 30093711, 28717674, 23542697, 29356177, 25366275, 27683934)

#	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, SCV003834327.2

#	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: Nov 10, 2024

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