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NM_175914.5(HNF4A):c.403C>T (p.Gln135Ter) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Feb 7, 2020
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:
RCV000520909.6

Allele description [Variation Report for NM_175914.5(HNF4A):c.403C>T (p.Gln135Ter)]

NM_175914.5(HNF4A):c.403C>T (p.Gln135Ter)

Gene:
HNF4A:hepatocyte nuclear factor 4 alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q13.12
Genomic location:
Preferred name:
NM_175914.5(HNF4A):c.403C>T (p.Gln135Ter)
Other names:
NM_175914.5(HNF4A):c.403C>T; p.Gln135Ter
HGVS:
  • NC_000020.11:g.44413777C>T
  • NG_009818.1:g.62977C>T
  • NM_000457.6:c.469C>T
  • NM_001030003.3:c.403C>T
  • NM_001030004.3:c.403C>T
  • NM_001258355.2:c.448C>T
  • NM_001287182.2:c.394C>T
  • NM_001287183.2:c.394C>T
  • NM_001287184.2:c.394C>T
  • NM_175914.5:c.403C>TMANE SELECT
  • NM_178849.3:c.469C>T
  • NM_178850.3:c.469C>T
  • NP_000448.3:p.Gln157Ter
  • NP_001025174.1:p.Gln135Ter
  • NP_001025175.1:p.Gln135Ter
  • NP_001245284.1:p.Gln150Ter
  • NP_001274111.1:p.Gln132Ter
  • NP_001274112.1:p.Gln132Ter
  • NP_001274113.1:p.Gln132Ter
  • NP_787110.2:p.Gln135Ter
  • NP_849180.1:p.Gln157Ter
  • NP_849181.1:p.Gln157Ter
  • LRG_483t1:c.403C>T
  • LRG_483:g.62977C>T
  • NC_000020.10:g.43042417C>T
  • NM_175914.3:c.403C>T
  • NM_175914.4:c.403C>T
Protein change:
Q132*
Links:
dbSNP: rs1555815158
NCBI 1000 Genomes Browser:
rs1555815158
Molecular consequence:
  • NM_000457.6:c.469C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001030003.3:c.403C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001030004.3:c.403C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001258355.2:c.448C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001287182.2:c.394C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001287183.2:c.394C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001287184.2:c.394C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_175914.5:c.403C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_178849.3:c.469C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_178850.3:c.469C>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
SCV000619403GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Feb 7, 2020) 		germlineclinical testing

Citation Link,

SCV002069297Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Nov 30, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot 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

Details of each submission

From GeneDx, SCV000619403.3

#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 in large population cohorts (Lek et al., 2016); 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 Genetic Services Laboratory, University of Chicago, SCV002069297.1

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

Description

DNA sequence analysis of the HNF4A gene demonstrated a sequence change, c.403C>T, which results in the creation of a premature stop codon at amino acid position 135, p.Gln135*. This sequence change is predicted to result in an abnormal transcript, which is likely to be degraded, or lead to the production of a truncated HNF4A protein with potentially abnormal function. This pathogenic sequence change has not been previously been described in the literature in patients with HNF4A-related diabetes, and is also absent from large population databases such as gnomAD.

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

Last Updated: Apr 20, 2024