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NM_001492.6(GDF1):c.889C>T (p.Gln297Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 7, 2018
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:
RCV002551545.9

Allele description [Variation Report for NM_001492.6(GDF1):c.889C>T (p.Gln297Ter)]

NM_001492.6(GDF1):c.889C>T (p.Gln297Ter)

Genes:
CERS1:ceramide synthase 1 [Gene - OMIM - HGNC]
GDF1:growth differentiation factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.11
Genomic location:
Preferred name:
NM_001492.6(GDF1):c.889C>T (p.Gln297Ter)
HGVS:
  • NC_000019.10:g.18868827G>A
  • NG_012070.1:g.32318C>T
  • NG_033056.1:g.32318C>T
  • NM_001387438.1:c.889C>T
  • NM_001387440.1:c.*1750C>T
  • NM_001492.6:c.889C>TMANE SELECT
  • NM_021267.5:c.*1158C>TMANE SELECT
  • NP_001374367.1:p.Gln297Ter
  • NP_001483.3:p.Gln297Ter
  • NC_000019.9:g.18979636G>A
Protein change:
Q297*
Links:
dbSNP: rs1466604623
NCBI 1000 Genomes Browser:
rs1466604623
Molecular consequence:
  • NM_001387440.1:c.*1750C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_021267.5:c.*1158C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001387438.1:c.889C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001492.6:c.889C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001585860Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 7, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV001585860.4

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

Description

For these reasons, this variant has been classified as Pathogenic. This sequence change results in a premature translational stop signal in the GDF1 gene (p.Gln297*). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 77 amino acids of the GDF1 protein. While this variant is not present in population databases, the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with GDF1-related disease. A different truncation (p.Phe349Leufs*35) that lies downstream of this variant has been determined to be likely pathogenic (Invitae). This suggests that deletion of this region of the GDF1 protein is causative of disease.

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

Last Updated: Sep 8, 2024