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NM_014028.4(OSTM1):c.415_416del (p.Gln140fs) AND Autosomal recessive osteopetrosis 5

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
May 8, 2023
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:
RCV000175853.9

Allele description [Variation Report for NM_014028.4(OSTM1):c.415_416del (p.Gln140fs)]

NM_014028.4(OSTM1):c.415_416del (p.Gln140fs)

Gene:
OSTM1:osteoclastogenesis associated transmembrane protein 1 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
6q21
Genomic location:
Preferred name:
NM_014028.4(OSTM1):c.415_416del (p.Gln140fs)
HGVS:
  • NC_000006.12:g.108064286CT[2]
  • NG_007262.1:g.15447AG[2]
  • NM_014028.4:c.415_416delMANE SELECT
  • NP_054747.2:p.Gln140fs
  • NC_000006.11:g.108385490CT[2]
  • NC_000006.11:g.108385490_108385491del
Protein change:
Q140fs
Links:
OMIM: 607649.0002; dbSNP: rs794727287
NCBI 1000 Genomes Browser:
rs794727287
Molecular consequence:
  • NM_014028.4:c.415_416del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Autosomal recessive osteopetrosis 5
Synonyms:
Osteopetrosis infantile malignant 3
Identifiers:
MONDO: MONDO:0009817; MedGen: C1968603; Orphanet: 85179; OMIM: 259720

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000023235OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2006)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV002020582Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 16, 2021)
germlineclinical testing

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

SCV003924297Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 8, 2023)
germlineresearch

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Identification of a novel mutation in the coding region of the grey-lethal gene OSTM1 in human malignant infantile osteopetrosis.

Ramírez A, Faupel J, Goebel I, Stiller A, Beyer S, Stöckle C, Hasan C, Bode U, Kornak U, Kubisch C.

Hum Mutat. 2004 May;23(5):471-6.

PubMed [citation]
PMID:
15108279

Importance of neurological assessment before bone marrow transplantation for osteopetrosis.

Abinun M, Newson T, Rowe PW, Flood TJ, Cant AJ.

Arch Dis Child. 1999 Mar;80(3):273-4.

PubMed [citation]
PMID:
10325711
PMCID:
PMC1717852
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000023235.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In a 3-month-old girl with malignant infantile osteopetrosis (259720), born of second-cousin Kuwaiti parents, Ramirez et al. (2004) identified a homozygous 2-bp deletion, 415delAG, in exon 2 of the OSTM1 gene. The parents were heterozygous for the mutation, which was not found in 100 German control chromosomes.

In a Kuwaiti boy previously described by Abinun et al. (1999) and an unrelated Kuwaiti girl, both with severe osteopetrosis, Pangrazio et al. (2006) identified homozygosity for the 415delAG mutation. Both sets of parents were consanguineous, and all were heterozygous for the mutation. Haplotype analysis indicated that the 3 Kuwaiti families found to carry this mutation to date are not related, although the authors noted that it is possible that they share a common ancestor.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV002020582.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV003924297.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024