Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_001127671.2(LIFR):c.1937C>A (p.Thr646Asn)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Likely benign(2);Likely pathogenic(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Sep 14, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000235543.11
Variation ID:
235543
Description:
single nucleotide variant
Help

NM_001127671.2(LIFR):c.1937C>A (p.Thr646Asn)

Allele ID
237224
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5p13.1
Genomic location
5: 38493734 (GRCh38) GRCh38 UCSC
5: 38493836 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.38493734G>T
NG_011817.1:g.106672C>A
NM_001127671.2:c.1937C>A MANE Select NP_001121143.1:p.Thr646Asn missense
... more HGVS
Protein change
T646N
Other names
-
Canonical SPDI
NC_000005.10:38493733:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00719 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00830
The Genome Aggregation Database (gnomAD) 0.00841
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00846
The Genome Aggregation Database (gnomAD) 0.00875
Trans-Omics for Precision Medicine (TOPMed) 0.00962
Exome Aggregation Consortium (ExAC) 0.00231
1000 Genomes Project 0.00719
Links
ClinGen: CA3242800
dbSNP: rs79040751
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000224818.7
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Aug 31, 2020 RCV000999980.4
Likely pathogenic 1 criteria provided, single submitter Sep 14, 2016 RCV000491876.2
Benign 1 criteria provided, single submitter Jun 29, 2018 RCV000505869.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LIFR - - GRCh38
GRCh37
522 554

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely Benign
(Jun 12, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281205.1
Submitted: (May 19, 2016)
Evidence details
Comment:
Converted during submission to Likely benign.
Likely pathogenic
(Sep 14, 2016)
criteria provided, single submitter
Method: research
Congenital anomalies of kidney and urinary tract
Allele origin: germline
Weber Lab,Hannover Medical School
Accession: SCV000346033.1
Submitted: (Sep 14, 2016)
Evidence details
Publications
PubMed (1)
Likely benign
(Aug 31, 2020)
criteria provided, single submitter
Method: clinical testing
Stüve-Wiedemann syndrome
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000604099.3
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Jun 29, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000862038.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Stüve-Wiedemann syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001318857.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001103028.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001868939.1
Submitted: (Sep 14, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28334964)

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
Mutations in the leukemia inhibitory factor receptor (LIFR) gene and Lifr deficiency cause urinary tract malformations. Kosfeld A Human molecular genetics 2017 PMID: 28334964
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=LIFR - - - -

Text-mined citations for rs79040751...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021