NM_003701.4(TNFSF11):c.107C>G (p.Pro36Arg) AND Autosomal recessive osteopetrosis 2

Germline classification:: Likely benign (1 submission)
Last evaluated:: Apr 27, 2017
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:: RCV000338886.5

Allele description [Variation Report for NM_003701.4(TNFSF11):c.107C>G (p.Pro36Arg)]

NM_003701.4(TNFSF11):c.107C>G (p.Pro36Arg)

Genes:

LOC130009662:ATAC-STARR-seq lymphoblastoid silent region 5301 [Gene]
TNFSF11:TNF superfamily member 11 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q14.11

Genomic location:

Preferred name:

NM_003701.4(TNFSF11):c.107C>G (p.Pro36Arg)

HGVS:

NC_000013.11:g.42574410C>G
NG_008990.1:g.16675C>G
NM_003701.4:c.107C>GMANE SELECT
NM_033012.4:c.-1+2672C>G
NP_003692.1:p.Pro36Arg
NC_000013.10:g.43148546C>G
NM_003701.3:c.107C>G

Protein change:

P36R

Links:

dbSNP: rs138818878

NCBI 1000 Genomes Browser:

rs138818878

Molecular consequence:

NM_033012.4:c.-1+2672C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_003701.4:c.107C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Autosomal recessive osteopetrosis 2
Synonyms:: OSTEOPETROSIS, MILD AUTOSOMAL RECESSIVE FORM; Osteopetrosis osteoclast-poor
Identifiers:: MONDO: MONDO:0009816; MedGen: C1850126; Orphanet: 667; OMIM: 259710

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000384466	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21541994, 20499338 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000384466

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Camurati-Engelmann disease: unique variant featuring a novel mutation in TGFβ1 encoding transforming growth factor beta 1 and a missense change in TNFSF11 encoding RANK ligand.

Whyte MP, Totty WG, Novack DV, Zhang X, Wenkert D, Mumm S.

J Bone Miner Res. 2011 May;26(5):920-33. doi: 10.1002/jbmr.283.

PubMed [citation]

PMID:: 21541994
PMCID:: PMC3179308

Dysosteosclerosis presents as an "osteoclast-poor" form of osteopetrosis: comprehensive investigation of a 3-year-old girl and literature review.

Whyte MP, Wenkert D, McAlister WH, Novack DV, Nenninger AR, Zhang X, Huskey M, Mumm S.

J Bone Miner Res. 2010 Nov;25(11):2527-39. doi: 10.1002/jbmr.131. Review.

PubMed [citation]

PMID:: 20499338
PMCID:: PMC3179286

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000384466.3

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

Description

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, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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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