NM_000451.4(SHOX):c.70G>A (p.Gly24Arg) AND not specified

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 16, 2024
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:: RCV002248197.2

Allele description [Variation Report for NM_000451.4(SHOX):c.70G>A (p.Gly24Arg)]

NM_000451.4(SHOX):c.70G>A (p.Gly24Arg)

Gene:

SHOX:SHOX homeobox [Gene - OMIM - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp22.33

Genomic location:

Preferred name:

NM_000451.4(SHOX):c.70G>A (p.Gly24Arg)

HGVS:

NC_000023.11:g.630967G>A
NC_000024.10:g.630967G>A
NG_009385.2:g.11624G>A
NM_000451.4:c.70G>AMANE SELECT
NM_006883.2:c.70G>A
NP_000442.1:p.Gly24Arg
NP_006874.1:p.Gly24Arg
LRG_710t1:c.70G>A
LRG_710t2:c.70G>A
LRG_710:g.11624G>A
LRG_710p1:p.Gly24Arg
LRG_710p2:p.Gly24Arg
NC_000023.10:g.591702G>A
NC_000024.9:g.541702G>A

Protein change:

G24R

Links:

dbSNP: rs761008675

NCBI 1000 Genomes Browser:

rs761008675

Molecular consequence:

NM_000451.4:c.70G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006883.2:c.70G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002519337	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Uncertain significance (May 4, 2022)	germline	clinical testing	Citation Link,
SCV005203502	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jul 16, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002519337

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2019)

Uncertain significance
(May 4, 2022)

germline

clinical testing

Citation Link,

SCV005203502

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jul 16, 2024)

germline

clinical testing

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

Citation Link

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

The novel human SHOX allelic variant database.

Niesler B, Röth R, Wilke S, Fujimura F, Fischer C, Rappold G.

Hum Mutat. 2007 Oct;28(10):933-8.

PubMed [citation]

PMID:: 17726696

Details of each submission

From Mendelics, SCV002519337.1

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

#	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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005203502.1

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

Description

Variant summary: SHOX c.70G>A (p.Gly24Arg) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 250888 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.70G>A has been reported in the literature in at least an individual affected with Short Stature (example: Niesler_2007). These report(s) do not provide unequivocal conclusions about association of the variant with Short Stature. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 17726696). ClinVar contains an entry for this variant (Variation ID: 1685105). Based on the evidence outlined above, the variant was classified as 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: Sep 29, 2024

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