NM_001384474.1(LOXHD1):c.2641G>A (p.Gly881Arg) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 29, 2024
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:: RCV002571592.2

Allele description [Variation Report for NM_001384474.1(LOXHD1):c.2641G>A (p.Gly881Arg)]

NM_001384474.1(LOXHD1):c.2641G>A (p.Gly881Arg)

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.2641G>A (p.Gly881Arg)

HGVS:

NC_000018.10:g.46560503C>T
NG_016646.2:g.101531G>A
NM_001384474.1:c.2641G>AMANE SELECT
NM_144612.7:c.2641G>A
NP_001371403.1:p.Gly881Arg
NP_653213.6:p.Gly881Arg
NC_000018.9:g.44140466C>T
NM_144612.6:c.2641G>A

Protein change:

G881R

Molecular consequence:

NM_001384474.1:c.2641G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_144612.7:c.2641G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003520450	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 29, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 29676012, 33753533, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003520450

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 29, 2024)

germline

clinical testing

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

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

Further audiovestibular characterization of DFNB77, caused by deleterious variants in LOXHD1, and investigation into the involvement of Fuchs corneal dystrophy.

Wesdorp M, Schreur V, Beynon AJ, Oostrik J, van de Kamp JM, Elting MW, van den Boogaard MH, Feenstra I, Admiraal RJC, Kunst HPM, Hoyng CB, Kremer H, Yntema HG, Pennings RJE, Schraders M.

Clin Genet. 2018 Aug;94(2):221-231. doi: 10.1111/cge.13368. Epub 2018 Jun 8.

PubMed [citation]

PMID:: 29676012

Rising of LOXHD1 as a signature causative gene of down-sloping hearing loss in people in their teens and 20s.

Kim BJ, Jeon HW, Jeon W, Han JH, Oh J, Yi N, Kim MY, Kim M, Kim JN, Kim BH, Hyon JY, Kim D, Koo JW, Oh DY, Choi BY.

J Med Genet. 2022 May;59(5):470-480. doi: 10.1136/jmedgenet-2020-107594. Epub 2021 Mar 22.

PubMed [citation]

PMID:: 33753533

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003520450.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 881 of the LOXHD1 protein (p.Gly881Arg). This variant is present in population databases (rs759837659, gnomAD 0.004%). This missense change has been observed in individual(s) with deafness (PMID: 29676012, 33753533; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1875098). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. For these reasons, this variant has been classified as Pathogenic.

#	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: Feb 20, 2024

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