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NM_175914.5(HNF4A):c.1321A>G (p.Ile441Val) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (6 submissions)
Last evaluated:
Oct 20, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV000725499.28

Allele description [Variation Report for NM_175914.5(HNF4A):c.1321A>G (p.Ile441Val)]

NM_175914.5(HNF4A):c.1321A>G (p.Ile441Val)

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.1321A>G (p.Ile441Val)
Other names:
NM_175914.5(HNF4A):c.1321A>G; p.Ile441Val
HGVS:
  • NC_000020.11:g.44429627A>G
  • NG_009818.1:g.78827A>G
  • NM_000457.6:c.1387A>G
  • NM_001030003.3:c.1291A>G
  • NM_001258355.2:c.1366A>G
  • NM_001287182.2:c.1282A>G
  • NM_001287183.2:c.1312A>G
  • NM_175914.5:c.1321A>GMANE SELECT
  • NM_178849.3:c.1357A>G
  • NP_000448.3:p.Ile463Val
  • NP_000448.3:p.Ile463Val
  • NP_001025174.1:p.Ile431Val
  • NP_001245284.1:p.Ile456Val
  • NP_001274111.1:p.Ile428Val
  • NP_001274112.1:p.Ile438Val
  • NP_787110.2:p.Ile441Val
  • NP_787110.2:p.Ile441Val
  • NP_849180.1:p.Ile453Val
  • LRG_483t1:c.1321A>G
  • LRG_483t2:c.1387A>G
  • LRG_483:g.78827A>G
  • LRG_483p1:p.Ile441Val
  • LRG_483p2:p.Ile463Val
  • NC_000020.10:g.43058267A>G
  • NM_000457.3:c.1387A>G
  • NM_000457.4:c.1387A>G
  • NM_000457.5:c.1387A>G
  • NM_175914.3:c.1321A>G
  • NM_175914.4:c.1321A>G
Protein change:
I428V
Links:
dbSNP: rs147638455
NCBI 1000 Genomes Browser:
rs147638455
Molecular consequence:
  • NM_000457.6:c.1387A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001030003.3:c.1291A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258355.2:c.1366A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001287182.2:c.1282A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001287183.2:c.1312A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_175914.5:c.1321A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_178849.3:c.1357A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
4

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
SCV000337348Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)
Uncertain significance
(Nov 16, 2015)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV000589599GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely benign
(May 5, 2021)
germlineclinical testing

Citation Link,

SCV001475904Athena Diagnostics Inc
criteria provided, single submitter

(Athena Diagnostics Criteria)
Likely benign
(Dec 13, 2019)
unknownclinical testing

PubMed (9)
[See all records that cite these PMIDs]

SCV001747309CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Benign
(Sep 1, 2023)
germlineclinical testing

Citation Link,

SCV002293203Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Oct 20, 2023)
germlineclinical testing

PubMed (9)
[See all records that cite these PMIDs]

SCV002503561AiLife Diagnostics, AiLife Diagnostics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Feb 21, 2021)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes3not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

Frequency of HNF4A-P.I463V Variant in the Tunisian North-African Population and Its Relation with Diabetes Mellitus.

Amara A, Ben Charfeddine I, Ghédir H, Mamaï O, Jemni-Yacoub S, Chaieb L, Saad A, Chadli-Chaieb M, Gribaa M.

Iran J Public Health. 2015 Mar;44(3):396-403.

PubMed [citation]
PMID:
25905084
PMCID:
PMC4402419

Novel mechanisms of regulation of the expression and transcriptional activity of hepatocyte nuclear factor 4α.

Guo S, Lu H.

J Cell Biochem. 2019 Jan;120(1):519-532. doi: 10.1002/jcb.27407. Epub 2018 Sep 7.

PubMed [citation]
PMID:
30191603
PMCID:
PMC7745837
See all PubMed Citations (17)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000337348.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000589599.3

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

Description

This variant is associated with the following publications: (PMID: 23227446, 27884173, 24097065, 25905084, 26059258, 10227563, 21105491, 10768098, 31264968, 31595705)

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

From Athena Diagnostics Inc, SCV001475904.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV001747309.14

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

HNF4A: BS1, BS2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From Invitae, SCV002293203.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)

Description

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 441 of the HNF4A protein (p.Ile441Val). This variant is present in population databases (rs147638455, gnomAD 0.07%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with maturity onset diabetes of the young (PMID: 10227563, 21105491, 23247789, 26059258, 31595705, 33846082, 34373539, 35256061). This variant is also known as p.Ile454Val, p.Ile463Val. ClinVar contains an entry for this variant (Variation ID: 36345). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on HNF4A protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

From AiLife Diagnostics, AiLife Diagnostics, SCV002503561.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (7)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Apr 15, 2024