LOXHD1

lipoxygenase homology PLAT domains 1

Basic information

Region (hg38): 18:46476972-46657220

Previous symbols: [ "DFNB77" ]

Links

ENSG00000167210 ∙ NCBI:125336 ∙ OMIM:613072 ∙ HGNC:26521 ∙ Uniprot:Q8IVV2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 33.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001384474.1	NP_001371403.1	41	yes	-
ENST00000642948.1	ENSP00000496347.1	41	yes	-
NM_144612.7	NP_653213.6	40	-	-
NM_001145472.3	NP_001138944.1	22	-	-

Phenotypes

GenCC

Source: genCC

• autosomal recessive nonsyndromic hearing loss 77 (Definitive), mode of inheritance: AR
• nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR
• Fuchs' endothelial dystrophy (Limited), mode of inheritance: AD
• autosomal recessive nonsyndromic hearing loss 77 (Strong), mode of inheritance: AR
• hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
• autosomal recessive nonsyndromic hearing loss 77 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 77	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic	19732867; 23226338

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LOXHD1 gene.

• not_provided (2227 variants)
• Autosomal_recessive_nonsyndromic_hearing_loss_77 (811 variants)
• Inborn_genetic_diseases (406 variants)
• not_specified (307 variants)
• LOXHD1-related_disorder (66 variants)
• Hearing_impairment (15 variants)
• Nonsyndromic_genetic_hearing_loss (13 variants)
• Rare_genetic_deafness (12 variants)
• Monogenic_hearing_loss (5 variants)
• Autosomal_dominant_nonsyndromic_hearing_loss (4 variants)
• Deafness (3 variants)
• VATER_association (2 variants)
• Variant_of_unknown_significance (1 variants)
• concomitant_exotropia (1 variants)
• Gastric_cancer (1 variants)
• Hearing_loss,_autosomal_recessive (1 variants)
• Stickler_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LOXHD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001384474.1. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			31	961	10	1002
missense		24	787	70	8	889
nonsense	65	75	1			141
start loss	1					1
frameshift	93	92	1	1		187
splice donor/acceptor (+/-2bp)	12	100	3			115
Total	171	291	823	1032	18

Highest pathogenic variant AF is 0.0010370275

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LOXHD1	protein_coding	protein_coding	ENST00000300591	22	180062

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	577	678	0.851	0.0000418	7398
Missense in Polyphen		351	432.11	0.8123		4862
Synonymous	1.61	245	279	0.878	0.0000194	2061
Loss of Function	1.47	46	58.1	0.792	0.00000314	621

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in hearing. Required for normal function of hair cells in the inner ear (By similarity). {ECO:0000250, ECO:0000269|PubMed:19732867}.
• Disease: DISEASE: Deafness, autosomal recessive, 77 (DFNB77) [MIM:613079]: A form of non-syndromic deafness characterized by preserved low- frequency hearing, and a trend toward mild to moderate mid- frequency and high-frequency hearing loss during childhood and adolescence. Hearing loss progresses to become moderate to severe at mid and high frequencies during adulthood. {ECO:0000269|PubMed:19732867}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: 1.18
• rvis_percentile_EVS: 92.83

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.868

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: sensory perception of sound;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: stereocilium
• Molecular function: catalase activity;heme binding