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NM_000515.5(GH1):c.406G>A (p.Val136Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Feb 20, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000197151.5
Variation ID:
197151
Description:
single nucleotide variant
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NM_000515.5(GH1):c.406G>A (p.Val136Ile)

Allele ID
194312
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q23.3
Genomic location
17: 63917810 (GRCh38) GRCh38 UCSC
17: 61995170 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P01241:p.Val136Ile
NC_000017.10:g.61995170C>T
NC_000017.11:g.63917810C>T
... more HGVS
Protein change
V136I, V121I, V96I
Other names
-
Canonical SPDI
NC_000017.11:63917809:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00561
The Genome Aggregation Database (gnomAD) 0.00526
The Genome Aggregation Database (gnomAD) 0.00560
Trans-Omics for Precision Medicine (TOPMed) 0.00582
1000 Genomes Project 0.00180
Exome Aggregation Consortium (ExAC) 0.00545
The Genome Aggregation Database (gnomAD), exomes 0.00571
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00746
Links
ClinGen: CA202715
UniProtKB: P01241#VAR_011919
dbSNP: rs5388
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 31, 2019 RCV000421927.4
Benign 1 criteria provided, single submitter Mar 30, 2015 RCV000178109.1
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001128609.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GH-LCR - - - GRCh38 - 875
GH1 - - GRCh38
GRCh37
8 114

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely Benign
(Jan 06, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000511102.1
Submitted: (Feb 17, 2017)
Evidence details
Comment:
Converted during submission to Likely benign.
Benign
(Mar 30, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230110.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001012284.2
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Growth hormone deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001288076.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)

Functional evidence

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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

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Title Author Journal Year Link
Variants in the GH-IGF axis confer susceptibility to lung cancer. Rudd MF Genome research 2006 PMID: 16741161
Novel mutations of the growth hormone 1 (GH1) gene disclosed by modulation of the clinical selection criteria for individuals with short stature. Millar DS Human mutation 2003 PMID: 12655557
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GH1 - - - -

Text-mined citations for rs5388...

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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