NM_014516.4(CNOT3):c.2209A>G (p.Lys737Glu) AND Intellectual developmental disorder with speech delay, autism, and dysmorphic facies

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 7, 2023
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:: RCV003232958.2

Allele description [Variation Report for NM_014516.4(CNOT3):c.2209A>G (p.Lys737Glu)]

NM_014516.4(CNOT3):c.2209A>G (p.Lys737Glu)

Genes:

CNOT3:CCR4-NOT transcription complex subunit 3 [Gene - OMIM - HGNC]
LENG1:leukocyte receptor cluster member 1 [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.42

Genomic location:

Preferred name:

NM_014516.4(CNOT3):c.2209A>G (p.Lys737Glu)

HGVS:

NC_000019.10:g.54155354A>G
NM_014516.4:c.2209A>GMANE SELECT
NM_024316.3:c.*367T>CMANE SELECT
NP_055331.1:p.Lys737Glu
NC_000019.9:g.54659092A>G

Protein change:

K737E

Molecular consequence:

NM_024316.3:c.*367T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_014516.4:c.2209A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
Identifiers:: MONDO: MONDO:0032864; MedGen: C5231456; OMIM: 618672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003929533	Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg	criteria provided, single submitter (Hauer et al. (Genet Med. 2018))	Likely pathogenic (Jun 7, 2023)	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

SCV003929533

Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg

criteria provided, single submitter

(Hauer et al. (Genet Med. 2018))

Likely pathogenic
(Jun 7, 2023)

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	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical relevance of systematic phenotyping and exome sequencing in patients with short stature.

Hauer NN, Popp B, Schoeller E, Schuhmann S, Heath KE, Hisado-Oliva A, Klinger P, Kraus C, Trautmann U, Zenker M, Zweier C, Wiesener A, Abou Jamra R, Kunstmann E, Wieczorek D, Uebe S, Ferrazzi F, Büttner C, Ekici AB, Rauch A, Sticht H, Dörr HG, et al.

Genet Med. 2018 Jun;20(6):630-638. doi: 10.1038/gim.2017.159. Epub 2017 Oct 12.

PubMed [citation]

PMID:: 29758562
PMCID:: PMC5993671

Details of each submission

From Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, SCV003929533.1

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

Description

This variant has been identified by standard clinical testing. de novo Selected ACMG criteria: Likely pathogenic (II):PP3;PP2;PM2;PS2

#	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		1	not provided	not provided	not provided

Last Updated: Sep 1, 2024

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