NM_000451.4(SHOX):c.870G>A (p.Leu290=) AND not specified

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Dec 6, 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:: RCV000251367.23

Allele description [Variation Report for NM_000451.4(SHOX):c.870G>A (p.Leu290=)]

NM_000451.4(SHOX):c.870G>A (p.Leu290=)

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.870G>A (p.Leu290=)

HGVS:

NC_000023.11:g.644627G>A
NC_000024.10:g.644627G>A
NG_009385.2:g.25284G>A
NM_000451.4:c.870G>AMANE SELECT
NM_006883.2:c.633+3540G>A
NP_000442.1:p.Leu290=
NP_000442.1:p.Leu290=
LRG_710t1:c.870G>A
LRG_710t2:c.633+3540G>A
LRG_710:g.25284G>A
LRG_710p1:p.Leu290=
NC_000023.10:g.605362G>A
NC_000024.9:g.555362G>A
NM_000451.3:c.870G>A

Links:

dbSNP: rs746391025

NCBI 1000 Genomes Browser:

rs746391025

Molecular consequence:

NM_006883.2:c.633+3540G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000451.4:c.870G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

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
SCV000231546	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Likely benign (Apr 14, 2016)	germline	clinical testing	Citation Link,
SCV000304376	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000615263	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	benign (Dec 4, 2024)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25659810, 26467025
SCV005884782	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Dec 6, 2024)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	3	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

SHOX gene variants: growth hormone/insulin-like growth factor-1 status and response to growth hormone treatment.

Shapiro S, Klein GW, Klein ML, Wallach EJ, Fen Y, Godbold JH, Rapaport R.

Horm Res Paediatr. 2015;83(1):26-35. doi: 10.1159/000365507. Epub 2015 Jan 31.

PubMed [citation]

PMID:: 25659810

See all PubMed Citations (3)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000231546.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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		3	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000304376.1

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

#	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 Athena Diagnostics, SCV000615263.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	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, SCV005884782.1

#	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

Last Updated: May 16, 2025

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