LHFPL5
Basic information
Region (hg38): 6:35797206-35845397
Previous symbols: [ "DFNB67" ]
Links
Phenotypes
GenCC
Source:
- autosomal recessive nonsyndromic hearing loss 67 (Strong), mode of inheritance: AR
- autosomal recessive nonsyndromic hearing loss 67 (Strong), mode of inheritance: AR
- hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
- nonsyndromic genetic hearing loss (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Deafness, autosomal recessive 67 | AR | Audiologic/Otolaryngologic | Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development | Audiologic/Otolaryngologic | 16752389; 16459341 |
ClinVar
This is a list of variants' phenotypes submitted to
- Autosomal recessive nonsyndromic hearing loss 67 (4 variants)
- Autosomal recessive non-syndromic intellectual disability;Autosomal recessive nonsyndromic hearing loss 67 (1 variants)
- not provided (1 variants)
- Hearing loss, autosomal recessive (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHFPL5 gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 11 | |||||
missense | 44 | 49 | ||||
nonsense | 4 | |||||
start loss | 1 | |||||
frameshift | 5 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 3 | 3 | ||||
non coding | 85 | 12 | 11 | 108 | ||
Total | 6 | 9 | 133 | 22 | 11 |
Highest pathogenic variant AF is 0.0000197
Variants in LHFPL5
This is a list of pathogenic ClinVar variants found in the LHFPL5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-35797242-T-C | not specified | Uncertain significance (May 11, 2022) | ||
6-35804978-G-A | Benign (Nov 12, 2018) | |||
6-35805334-G-T | Autosomal recessive nonsyndromic hearing loss 67 | Uncertain significance (Jan 13, 2018) | ||
6-35805336-A-G | Autosomal recessive nonsyndromic hearing loss 67 | Uncertain significance (Jan 12, 2018) | ||
6-35805366-G-A | Autosomal recessive nonsyndromic hearing loss 67 | Uncertain significance (Jan 12, 2018) | ||
6-35805372-AAG-A | Hearing loss, autosomal recessive | Benign/Likely benign (Nov 05, 2019) | ||
6-35805510-A-G | Autosomal recessive nonsyndromic hearing loss 67 | Uncertain significance (Jan 13, 2018) | ||
6-35805539-A-G | Autosomal recessive nonsyndromic hearing loss 67 | Conflicting classifications of pathogenicity (Sep 02, 2019) | ||
6-35805543-C-T | Autosomal recessive nonsyndromic hearing loss 67 | Conflicting classifications of pathogenicity (Aug 23, 2018) | ||
6-35805578-C-T | Autosomal recessive nonsyndromic hearing loss 67 | Uncertain significance (Jan 13, 2018) | ||
6-35805608-C-G | Autosomal recessive nonsyndromic hearing loss 67 | Uncertain significance (Jan 13, 2018) | ||
6-35805641-G-C | Autosomal recessive nonsyndromic hearing loss 67 | Uncertain significance (Jan 12, 2018) | ||
6-35805671-A-G | Autosomal recessive nonsyndromic hearing loss 67 | Likely pathogenic (Aug 01, 2020) | ||
6-35805707-A-G | Uncertain significance (Jun 17, 2024) | |||
6-35805713-C-T | not specified • Autosomal recessive nonsyndromic hearing loss 67 | Conflicting classifications of pathogenicity (Dec 18, 2024) | ||
6-35805715-T-C | Likely benign (Jan 30, 2023) | |||
6-35805723-A-G | Autosomal recessive nonsyndromic hearing loss 67 | Likely pathogenic (Jan 09, 2025) | ||
6-35805729-G-A | Inborn genetic diseases | Uncertain significance (Oct 21, 2024) | ||
6-35805743-G-T | Uncertain significance (Jan 10, 2024) | |||
6-35805752-A-T | Autosomal recessive nonsyndromic hearing loss 67 | Uncertain significance (Jan 12, 2018) | ||
6-35805755-T-TG | Rare genetic deafness | Likely pathogenic (Apr 17, 2018) | ||
6-35805767-A-C | Uncertain significance (May 21, 2019) | |||
6-35805796-C-A | Likely benign (Jan 13, 2025) | |||
6-35805809-C-A | Nonsyndromic genetic hearing loss | Uncertain significance (Mar 03, 2022) | ||
6-35805810-C-A | Autosomal recessive nonsyndromic hearing loss 67 | Uncertain significance (Jan 13, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
LHFPL5 | protein_coding | protein_coding | ENST00000360215 | 3 | 28582 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000402 | 0.652 | 125729 | 0 | 19 | 125748 | 0.0000756 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.300 | 124 | 134 | 0.927 | 0.00000913 | 1430 |
Missense in Polyphen | 56 | 64.621 | 0.86659 | 702 | ||
Synonymous | 1.29 | 46 | 58.5 | 0.786 | 0.00000458 | 450 |
Loss of Function | 0.724 | 6 | 8.24 | 0.728 | 4.43e-7 | 86 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000202 | 0.000202 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000463 | 0.0000462 |
European (Non-Finnish) | 0.0000793 | 0.0000791 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: In the inner ear, may be a component of the hair cell's mechanotransduction machinery that functionally couples PCDH15 to the transduction channel. Regulates transducer channel conductance and is required for fast channel adaptation (By similarity). {ECO:0000250}.;
- Disease
- DISEASE: Deafness, autosomal recessive, 67 (DFNB67) [MIM:610265]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:16459341, ECO:0000269|PubMed:16752389, ECO:0000269|PubMed:26437881, ECO:0000269|PubMed:28281779}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.138
Intolerance Scores
- loftool
- 0.285
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- 0.151
- hipred
- N
- hipred_score
- 0.492
- ghis
- 0.485
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.306
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lhfpl5
- Phenotype
- hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- lhfpl5a
- Affected structure
- musculoskeletal movement
- Phenotype tag
- abnormal
- Phenotype quality
- quality
Gene ontology
- Biological process
- ion transport
- Cellular component
- plasma membrane;integral component of membrane
- Molecular function
- protein binding