rs111033258
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Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 12P and 1B. PM1PM2PP5_Very_StrongBP4
The NM_174878.3(CLRN1):c.144T>G(p.Asn48Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,614,134 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 1 hom. )
Consequence
CLRN1
NM_174878.3 missense
NM_174878.3 missense
Scores
3
9
7
Clinical Significance
Conservation
PhyloP100: -0.181
Genes affected
CLRN1 (HGNC:12605): (clarin 1) This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PM1
In a chain Clarin-1 (size 231) in uniprot entity CLRN1_HUMAN there are 22 pathogenic changes around while only 1 benign (96%) in NM_174878.3
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-150972565-A-C is Pathogenic according to our data. Variant chr3-150972565-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 4395.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-150972565-A-C is described in Lovd as [Pathogenic]. Variant chr3-150972565-A-C is described in Lovd as [Likely_pathogenic].
BP4
Computational evidence support a benign effect (MetaRNN=0.022752553). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CLRN1 | NM_174878.3 | c.144T>G | p.Asn48Lys | missense_variant | 1/3 | ENST00000327047.6 | NP_777367.1 | |
| CLRN1 | NM_001195794.1 | c.144T>G | p.Asn48Lys | missense_variant | 1/4 | NP_001182723.1 | ||
| CLRN1 | NM_001256819.2 | c.144T>G | p.Asn48Lys | missense_variant | 1/4 | NP_001243748.1 | ||
| CLRN1 | NR_046380.3 | n.163T>G | non_coding_transcript_exon_variant | 1/5 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CLRN1 | ENST00000327047.6 | c.144T>G | p.Asn48Lys | missense_variant | 1/3 | 1 | NM_174878.3 | ENSP00000322280 | P1 | |
| ENST00000469268.1 | n.236-29009A>C | intron_variant, non_coding_transcript_variant | 4 | |||||||
| CLRN1-AS1 | ENST00000476886.5 | n.124-90361A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes 0.000151 AC: 23AN: 152240Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000270 AC: 68AN: 251460Hom.: 1 AF XY: 0.000191 AC XY: 26AN XY: 135902
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GnomAD4 exome AF: 0.000136 AC: 199AN: 1461894Hom.: 1 Cov.: 31 AF XY: 0.000125 AC XY: 91AN XY: 727248
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GnomAD4 genome 0.000151 AC: 23AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74380
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:20Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Usher syndrome type 3 Pathogenic:7
| Pathogenic, no assertion criteria provided | research | Sharon lab, Hadassah-Hebrew University Medical Center | Jun 23, 2019 | - - |
| Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2003 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Dec 09, 2019 | NM_174878.2(CLRN1):c.144T>G(N48K) is classified as pathogenic in the context of Usher syndrome type 3. Sources cited for classification include the following: PMID 12080385, 12145752, 18281613, 19753315, 14569126 and12145752. Classification of NM_174878.2(CLRN1):c.144T>G(N48K) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals | Feb 01, 2019 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Nov 03, 2016 | Variant summary: The CLRN1 c.144T>G (p.Asn48Lys) variant involves the alteration of a non-conserved nucleotide. 4/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 25/121408 control chromosomes at a frequency of 0.0002059, which does not exceed the estimated maximal expected allele frequency of a pathogenic CLRN1 variant (0.0033541). This variant has been frequently reported in Jewish USH3 patients and was suggested to be a founder mutation in Ashkenazi Jews. In vitro and in vivo studies showed that this variant leads to mislocalization of CLRN1, disruption of the hair bundle integrity, and hearing loss phenotype (Geng_2012). In addition, one clinical diagnostic laboratory classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 27, 2018 | The CLRN1 c.144T>G (p.Asn48Lys) variant is well described in the literature as a common pathogenic variant for Usher syndrome in the Ashkenazi Jewish population. Across four studies, the p.Asn48Lys variant was detected in a total of 38 individuals with Usher syndrome, including in 33 homozygotes, in two compound heterozygotes, and in three heterozygotes (Adato et al. 2002; Fields et al. 2002; Ness et al. 2003; Herrera et al. 2008). Haplotype analysis suggests a founder effect for this variant. The variant was detected in 4/1,059 control chromosomes and is reported at a frequency of 0.005381 in the Ashkenazi Jewish population of the Genome Aggregation Database. The p.Asp48Asn variant is conserved and disrupts the only N-glycosylation site in the protein. In vitro functional studies demonstrated that the variant results in misfolding, mislocalization and degradation of the protein, and an absence of the actin reorganizing function (Tian et al. 2009). Gopal et al. (2015) used transgenic zebrafish to show that the variant causes aberrant hair cell bundle morphology with diminished function. The variant protein mislocalizes to the cell body with only a small amount reaching the hair bundle. Based on the evidence, the p.Asp48Asn variant is classified as pathogenic for Usher syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
not provided Pathogenic:4
| Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The CLRN1 p.Asn48Lys variant was identified in 60 of 162 proband chromosomes (frequency: 0.37) from individuals or families with Usher Syndrome type IIIa and retinitis pigmentosa (RP) and was only identified in 3 of 838 chromosomes (frequency: 0.004) from healthy controls (Herrera_2008_PMID:18281613; Sadeghi_2005_PMID:16028794; Ness_2003_PMID:14569126). The variant was also identified in dbSNP (ID: rs111033258), LOVD 3.0 and in ClinVar (classified as pathogenic for Usher syndrome type 3A by Laboratory for Molecular Medicine, Illumina, GeneDx, Counsyl, ARUP Laboratories, Integrated Genetics and OMIM, likely pathogenic by NIHR Bioresource Rare Diseases and a VUS for dominant RP by Illumina Clinical Services Laboratory). The variant was found in control databases in 68 of 251460 chromosomes (1 homozygous) at a frequency of 0.00027 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Ashkenazi Jewish in 58 of 10080 chromosomes (freq: 0.005754), Other in 1 of 6134 chromosomes (freq: 0.000163) and European (non-Finnish) in 9 of 113742 chromosomes (freq: 0.000079); it was not observed in the African, Latino, East Asian, European (Finnish) and South Asian populations. The N48K variant was identified in the homozygous state in a patient with RP and hearing loss and in the compound heterozygous state in a patient with hearing loss starting at age 7 (Tian_2009_PMID:19423712). Functional studies demonstrated that N48K mutants lacked N-linked glycosylation which led to misfolding, mislocalization, and degradation of the CLRN1 protein (Tian_2009_PMID:19423712). Animal models of the N48K variant in zebrafish and mice have also shown impaired CLRN1 localization and abnormal cochlear hair bundle morphology and function (Gopal_2005_ PMID:26180195; Geng_2012_PMID:22782034; Isosomppi_2009_PMID:19753315). The variant occurs outside of the splicing consensus sequence however 3 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE) predict the loss of a 3' splice site; however this is not a known splice site. The p.Asn48 residue is conserved across mammals and other organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, MutationTaster) suggest that the variant may impact the protein. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 24, 2023 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 48 of the CLRN1 protein (p.Asn48Lys). This variant is present in population databases (rs111033258, gnomAD 0.5%). This missense change has been observed in individuals with CLRN1-related conditions (PMID: 12080385, 14569126, 18281613). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 4395). 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 disruptive. Experimental studies have shown that this missense change affects CLRN1 function (PMID: 22787034, 26180195). For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Oct 28, 2021 | Reported as the most common pathogenic variant in the CLRN1 gene among North Americans and is reported as a founder mutation in the Ashkenazi Jewish population (Adato et al., 2002; Herrera et al., 2008; Geng et al., 2012); Published functional studies demonstrate impaired Clrn1 protein localization to the cochlear hair cell bundle (Geng et al., 2012); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 12145752, 28041643, 25262649, 12080385, 22787034, 18281613, 14569126, 19423712, 26180195, 29490346, 31097578, 25333069, 28559085, 30924848, 31370859, 31456290, 31980526) - |
Usher syndrome type 3A Pathogenic:3
| Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
| Pathogenic, criteria provided, single submitter | research | Ocular Genomics Institute, Massachusetts Eye and Ear | Apr 08, 2021 | The CLRN1 c.144T>G variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PS3, PP1-S, PM2, PM3. Based on this evidence we have classified this variant as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | curation | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | May 04, 2022 | The homozygous p.Asn48Lys variant in CLRN1 was identified by our study in 1 individual with Usher syndrome type 3A. The variant has been reported in at least 20 Ashkenazi Jewish individuals with Usher syndrome type 3A (PMID: 12080385, 145691260), segregated with disease in 12 affected relatives from 7 families (PMID: 145691260), and has been identified in 0.6% (58/10080) of Ashkenazi Jewish chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs111033258). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. This variant has also been reported in ClinVar (Variation ID: 4395) as pathogenic by many submitters, as likely pathogenic by NIHR Bioresource Rare Diseases, University of Cambridge, and as having uncertain significance by Illumina Clinical Services Laboratory. Animal models in mice and zebrafish have shown that this variant causes Usher syndrome type 3A (PMID: 26180195, 22787034). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. The presence of this variant in at least 20 affected homozygotes and in at least 20 individuals with Usher syndrome type 3A increases the likelihood that the p.Asn48Lys variant is pathogenic (PMID: 12080385, 145691260). In summary, this variant meets criteria to be classified as pathogenic for Usher syndrome type 3A in an autosomal recessive manner based on its homozygous occurrence and expected segregation pattern in affected individuals and families, as well as functional evidence that shows a damaging effect. ACMG/AMP Criteria applied: PS3, PP1_strong, PM3 (Richards 2015). - |
Retinitis pigmentosa Pathogenic:2
| Likely pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | Jan 01, 2015 | - - |
| Pathogenic, criteria provided, single submitter | curation | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | Apr 01, 2021 | The p.Asn48Lys variant in CLRN1 was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PS3, PP1-S, PM2, PM3. Based on this evidence we have classified this variant as Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab. - |
not specified Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 07, 2018 | The p.Asn48Lys variant (rs111033258; ClinVar variation ID: 4395) is a well-studied variant known to be causative of Usher syndrome, type 3A (USH3A, MIM: 276902); a disorder characterized by progressive hearing loss, retinitis pigmentosa, and variable peripheral vestibular dysfunction. This variant is thought to be an Ashkenazi Jewish (AJ) founder variant as is present in the AJ population at an estimated allele frequency of 0.35% (Ness 2003) through 0.53% (Genome Aggregation Database (gnomAD) browser). While often observed in homozygosity in AJ Usher patients, it has also been observed in heterozygosity with other pathogenic CLRN1 variants (Adato 2002, Fields 2002, Ness 2003, Herrera 2008. Isosomppi 2009). The asparagine at codon 48 had been experimentally demonstrated to be the sole site of glycosylation on the CLRN1 protein, which may explain the changes in protein localization and stability associated with p.Asn48Lys variant protein (Isosomppi 2000, Tian 2009, Geng 2012). Stable expression of p.Asn48Lys in a Zebrafish model also recapitulates the mis-location of variant protein (Gopal 2015). Finally, a mouse knock-in model of USH3A has demonstrated that mice homozygous for p.Asn48Lys have disrupted hair bundle organization and experience hearing loss by postnatal day 24 to a degree indistinguishable from homozygous CLRN1 knock out mice (Geng 2012). Taken together, we interpret the p.Asn48Lys variant as pathogenic. - |
Retinitis pigmentosa;C3280041:Retinitis pigmentosa 61;C5779850:Usher syndrome type 3A Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 12, 2022 | - - |
Retinitis pigmentosa 61 Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 28, 2024 | - - |
Retinal dystrophy Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Nov 22, 2018 | - - |
Retinitis pigmentosa;C5779850:Usher syndrome type 3A Other:1
| not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpreted as Pathogenic and reported on 05-12-2021 by Lab or GTR ID 500188. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
A;A
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;.
REVEL
Uncertain
Sift
Pathogenic
D;D;.
Sift4G
Pathogenic
D;D;.
Polyphen
D;.;.
Vest4
MutPred
Loss of sheet (P = 3e-04);Loss of sheet (P = 3e-04);.;
MVP
MPC
0.19
ClinPred
T
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Varity_R
gMVP
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at