NM_000163.5(GHR):c.491T>C (p.Leu164Ser) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 14, 2022
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:: RCV001908853.4

Allele description

NM_000163.5(GHR):c.491T>C (p.Leu164Ser)

Gene:

GHR:growth hormone receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5p12

Genomic location:

Preferred name:

NM_000163.5(GHR):c.491T>C (p.Leu164Ser)

HGVS:

NC_000005.10:g.42699875T>C
NG_011688.2:g.280952T>C
NM_000163.5:c.491T>CMANE SELECT
NM_001242399.2:c.512T>C
NM_001242400.2:c.491T>C
NM_001242401.4:c.491T>C
NM_001242402.2:c.491T>C
NM_001242403.3:c.491T>C
NM_001242404.2:c.491T>C
NM_001242405.2:c.491T>C
NM_001242406.2:c.491T>C
NM_001242460.2:c.425T>C
NM_001242462.1:c.491T>C
NP_000154.1:p.Leu164Ser
NP_001229328.1:p.Leu171Ser
NP_001229329.1:p.Leu164Ser
NP_001229330.1:p.Leu164Ser
NP_001229331.1:p.Leu164Ser
NP_001229332.1:p.Leu164Ser
NP_001229333.1:p.Leu164Ser
NP_001229334.1:p.Leu164Ser
NP_001229335.1:p.Leu164Ser
NP_001229389.1:p.Leu142Ser
NP_001229389.1:p.Leu142Ser
NP_001229391.1:p.Leu164Ser
NC_000005.9:g.42699977T>C
NM_001242460.1:c.425T>C

Protein change:

L142S

Links:

dbSNP: rs1757848305

NCBI 1000 Genomes Browser:

rs1757848305

Molecular consequence:

NM_000163.5:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242399.2:c.512T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242400.2:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242401.4:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242402.2:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242403.3:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242404.2:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242405.2:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242406.2:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242460.2:c.425T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001242462.1:c.491T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens ecotropic viral integration site 5-like protein-like (EVI5L) mRNA, ...
Homo sapiens ecotropic viral integration site 5-like protein-like (EVI5L) mRNA, partial sequence, alternatively spliced
gi|306415668|gb|HM370400.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002169091	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 14, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002169091

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 14, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002169091.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces leucine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 164 of the GHR protein (p.Leu164Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GHR-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 30, 2023

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