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NM_001384474.1(LOXHD1):c.2497C>T (p.Arg833Ter) AND Autosomal recessive nonsyndromic hearing loss 77

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
May 22, 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:
RCV000778910.11

Allele description [Variation Report for NM_001384474.1(LOXHD1):c.2497C>T (p.Arg833Ter)]

NM_001384474.1(LOXHD1):c.2497C>T (p.Arg833Ter)

Gene:
LOXHD1:lipoxygenase homology PLAT domains 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q21.1
Genomic location:
Preferred name:
NM_001384474.1(LOXHD1):c.2497C>T (p.Arg833Ter)
HGVS:
  • NC_000018.10:g.46563166G>A
  • NG_016646.2:g.98868C>T
  • NM_001384474.1:c.2497C>TMANE SELECT
  • NM_144612.7:c.2497C>T
  • NP_001371403.1:p.Arg833Ter
  • NP_653213.6:p.Arg833Ter
  • NP_653213.6:p.Arg833Ter
  • NC_000018.9:g.44143129G>A
  • NM_144612.6:c.2497C>T
  • c.2497C>T
  • p.Arg833X
Protein change:
R833*
Links:
dbSNP: rs188119157
NCBI 1000 Genomes Browser:
rs188119157
Molecular consequence:
  • NM_001384474.1:c.2497C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_144612.7:c.2497C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Autosomal recessive nonsyndromic hearing loss 77
Synonyms:
Deafness, autosomal recessive 77
Identifiers:
MONDO: MONDO:0013119; MedGen: C2746083; Orphanet: 90636; OMIM: 613079

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002588781DASA
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Nov 3, 2022) 		germlineclinical testing

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

SCV005652071Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(May 22, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

Details of each submission

From DASA, SCV002588781.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The c.2497C>T;p.(Arg833*) variant creates a premature translational stop signal in the LOXHD1 gene. It is expected to result in an absent or disrupted protein product - PVS1. ClinVar contains an entry for this variant (ClinVar ID: 47930) - PS4_supporting. The variant is present at low allele frequencies population databases (rs188119157 – gnomAD 0.0002529%; ABraOM no frequency - https://abraom.ib.usp.br/) - PM2_supporting. In summary, the currently available evidence indicates that the variant is pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV005652071.1

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

Last Updated: Apr 28, 2025