NM_015213.4(DENND5A):c.3647del (p.Gly1216fs) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 14, 2022
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:: RCV002658280.2

Allele description

NM_015213.4(DENND5A):c.3647del (p.Gly1216fs)

Gene:

DENND5A:DENN domain containing 5A [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_015213.4(DENND5A):c.3647del (p.Gly1216fs)

HGVS:

NC_000011.10:g.9141974del
NG_053019.1:g.128363del
NM_001243254.2:c.3646+1del
NM_001348748.1:c.3646delG
NM_001348749.2:c.3575del
NM_001348750.2:c.3359del
NM_015213.4:c.3647delMANE SELECT
NP_001335677.1:p.Gly1216Alafs
NP_001335678.1:p.Gly1192fs
NP_001335679.1:p.Gly1120fs
NP_056028.2:p.Gly1216fs
NC_000011.9:g.9163520del
NC_000011.9:g.9163521del
NR_145966.2:n.3821del

Protein change:

G1120fs

Molecular consequence:

NM_001348748.1:c.3646delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001348749.2:c.3575del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001348750.2:c.3359del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015213.4:c.3647del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_145966.2:n.3821del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001243254.2:c.3646+1del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus
Mus musculus
Classification of Antipsychotic Drugs by Gene Expression in the Frontal Cortex of Mice

BioProject
Mus musculus olfactory receptor family 5 subfamily J member 1 (Or5j1), mRNA
Mus musculus olfactory receptor family 5 subfamily J member 1 (Or5j1), mRNA
gi|289629183|ref|NM_146752.2|

Nucleotide
CBTC611.rev NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8932788 3', ...
CBTC611.rev NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8932788 3', mRNA sequence
gi|126268305|gnl|dbEST|45042132|gb| 580.1|

Nucleotide
Concise Conserved Domain Links for Protein (Select 1698997) (1)
Conserved Domains
hypothetical protein [Fibrobacter sp. UWB10]
hypothetical protein [Fibrobacter sp. UWB10]
gi|2509286508|ref|WP_283430270.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002974087	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 14, 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

SCV002974087

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 14, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Details of each submission

From Invitae, SCV002974087.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with DENND5A-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Gly1216Alafs*38) in the DENND5A gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 72 amino acid(s) of the DENND5A protein.

#	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: Feb 28, 2024

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