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NM_021008.4(DEAF1):c.553C>T (p.Gln185Ter) AND not provided

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
Oct 26, 2022
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:
RCV001780924.7

Allele description [Variation Report for NM_021008.4(DEAF1):c.553C>T (p.Gln185Ter)]

NM_021008.4(DEAF1):c.553C>T (p.Gln185Ter)

Gene:
DEAF1:DEAF1 transcription factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.5
Genomic location:
Preferred name:
NM_021008.4(DEAF1):c.553C>T (p.Gln185Ter)
HGVS:
  • NC_000011.10:g.688022G>A
  • NG_034156.2:g.24062C>T
  • NM_001293634.1:c.553C>T
  • NM_001367390.1:c.-174C>T
  • NM_021008.4:c.553C>TMANE SELECT
  • NP_001280563.1:p.Gln185Ter
  • NP_066288.2:p.Gln185Ter
  • NC_000011.9:g.688022G>A
  • NM_021008.2:c.553C>T
  • NM_021008.3:c.553C>T
Protein change:
Q185*
Links:
dbSNP: rs1860672898
NCBI 1000 Genomes Browser:
rs1860672898
Molecular consequence:
  • NM_001367390.1:c.-174C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001293634.1:c.553C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_021008.4:c.553C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002024037Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(May 12, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002584371GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely pathogenic
(Oct 15, 2022)
germlineclinical testing

Citation Link,

SCV004531026Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Oct 26, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

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
See all PubMed Citations (3)

Details of each submission

From Revvity Omics, Revvity, SCV002024037.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV002584371.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV004531026.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1324219). This variant has not been reported in the literature in individuals affected with DEAF1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln185*) 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).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 16, 2024