NM_021008.4(DEAF1):c.926del (p.Leu309fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 30, 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:: RCV003089145.4

Allele description [Variation Report for NM_021008.4(DEAF1):c.926del (p.Leu309fs)]

NM_021008.4(DEAF1):c.926del (p.Leu309fs)

Gene:

DEAF1:DEAF1 transcription factor [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11p15.5

Genomic location:

Preferred name:

NM_021008.4(DEAF1):c.926del (p.Leu309fs)

HGVS:

NC_000011.10:g.681034del
NG_034156.2:g.31050del
NM_001293634.1:c.731-1218del
NM_001367390.1:c.200del
NM_021008.4:c.926delMANE SELECT
NP_001354319.1:p.Leu67fs
NP_066288.2:p.Leu309fs
NC_000011.9:g.681034del
NM_021008.3:c.926delT

Protein change:

L309fs

Links:

dbSNP: rs1417226023

NCBI 1000 Genomes Browser:

rs1417226023

Molecular consequence:

NM_001367390.1:c.200del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_021008.4:c.926del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001293634.1:c.731-1218del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003021741	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 30, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30923367, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003021741

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 30, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

De novo and biallelic DEAF1 variants cause a phenotypic spectrum.

Nabais Sá MJ, Jensik PJ, McGee SR, Parker MJ, Lahiri N, McNeil EP, Kroes HY, Hagerman RJ, Harrison RE, Montgomery T, Splitt M, Palmer EE, Sachdev RK, Mefford HC, Scott AA, Martinez-Agosto JA, Lorenz R, Orenstein N, Berg JN, Amiel J, Heron D, Keren B, et al.

Genet Med. 2019 Sep;21(9):2059-2069. doi: 10.1038/s41436-019-0473-6. Epub 2019 Mar 29.

PubMed [citation]

PMID:: 30923367

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003021741.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Leu309Argfs*6) in the DEAF1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DEAF1 are known to be pathogenic (PMID: 30923367). This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with DEAF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1677014). For these reasons, this variant has been classified as Pathogenic.

#	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 16, 2025

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