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NM_144612.6(LOXHD1):c.4714C>T

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Mar 28, 2019)
Last evaluated:
Dec 11, 2018
Accession:
VCV000030990.4
Variation ID:
30990
Description:
single nucleotide variant
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NM_144612.6(LOXHD1):c.4714C>T (p.Arg1572Ter)

Allele ID
39947
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
18q21.1
Genomic location
18: 46524734 (GRCh38) GRCh38 UCSC
18: 44104697 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000018.10:g.46524734G>A
NC_000018.9:g.44104697G>A
NM_001145472.3:c.1381C>T NP_001138944.1:p.Arg461Ter nonsense
... more HGVS
Protein change
R1572*
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
0.01817 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00006
Links
ClinGen: CA259968
OMIM: 613072.0002
dbSNP: rs75949023
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Oct 31, 2018 RCV000023981.6
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Dec 11, 2018 RCV000627214.2
Pathogenic 1 criteria provided, single submitter Jul 15, 2014 RCV000211793.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LOXHD1 - - GRCh38
GRCh37
410 450

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 77
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893496.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Likely pathogenic
(Mar 08, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000748201.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The R1572X variant in the LOXHD1 gene has been reported previously in two unrelated Ashkenazi Jewish families with autosomal recessive nonsyndromic hearing loss, however, affected ... (more)
Likely pathogenic
(Oct 22, 2018)
criteria provided, single submitter
Method: clinical testing
Deafness, autosomal recessive 77
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000914816.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (3)
Comment:
The LOXHD1 c.4714C>T (p.Arg1572Ter) variant is a stop-gained variant that is predicted to cause a premature truncation of the protein. The p.Arg1572Ter variant has been ... (more)
Pathogenic
(Dec 11, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000954684.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change creates a premature translational stop signal (p.Arg1572*) in the LOXHD1 gene. It is expected to result in an absent or disrupted protein ... (more)
Pathogenic
(Jul 15, 2014)
criteria provided, single submitter
Method: clinical testing
Rare genetic deafness
Allele origin: germline
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine
Accession: SCV000221196.4
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
The p.Arg1572X variant in LOXHD1 has been reported in 2 homozygous Ashkenazi Jew ish individuals with nonsyndromic hearing loss, and it was found to segregate ... (more)
Pathogenic
(May 01, 2011)
no assertion criteria provided
Method: literature only
DEAFNESS, AUTOSOMAL RECESSIVE 77
Allele origin: germline
OMIM
Accession: SCV000045272.1
Submitted: (Apr 25, 2012)
Evidence details
Publications
PubMed (1)

Citations for this variant

Title Author Journal Year Link
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 Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Disease variants in genomes of 44 centenarians. Freudenberg-Hua Y Molecular genetics & genomic medicine 2014 PMID: 25333069
PECONPI: a novel software for uncovering pathogenic copy number variations in non-syndromic sensorineural hearing loss and other genetically heterogeneous disorders. Tsai EA American journal of medical genetics. Part A 2013 PMID: 23897863
A deleterious mutation in the LOXHD1 gene causes autosomal recessive hearing loss in Ashkenazi Jews. Edvardson S American journal of medical genetics. Part A 2011 PMID: 21465660

Record last updated Oct 27, 2019