rs111033258

Positions:

• chr3-150972565-A-C

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 14P and 1B. PM1 PM2 PM5 PP5_Very_Strong BP4

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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N48D) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00015 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00014 (1 hom.)
• Consequence: CLRN1 NM_174878.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:21 O:1
• 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]

(HGNC:):

CLRN1-AS1 (HGNC:30895): (CLRN1 antisense RNA 1)

ACMG classification

Verdict is Pathogenic. Variant got 13 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_174878.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-150972567-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 48143.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=2}.
• 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	UniProt
CLRN1	NM_174878.3	c.144T>G	p.Asn48Lys	missense_variant	1/3	ENST00000327047.6
CLRN1	NM_001195794.1	c.144T>G	p.Asn48Lys	missense_variant	1/4
CLRN1	NM_001256819.2	c.144T>G	p.Asn48Lys	missense_variant	1/4
CLRN1	NR_046380.3	n.163T>G		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLRN1	ENST00000327047.6	c.144T>G	p.Asn48Lys	missense_variant	1/3	1	NM_174878.3	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 AF: 0.000151 AC: 23 AN: 152240 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000270 AC: 68 AN: 251460 Hom.: 1 AF XY: 0.000191 AC XY: 26 AN XY: 135902

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00575

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000791

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000136 AC: 199 AN: 1461894 Hom.: 1 Cov.: 31 AF XY: 0.000125 AC XY: 91 AN XY: 727248

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00593

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000216

Gnomad4 OTH exome AF: 0.000331

GnomAD4 genome AF: 0.000151 AC: 23 AN: 152240 Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13 AN XY: 74380

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000638 Hom.: 0

Bravo AF: 0.000151

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.000206 AC: 25

EpiCase AF: 0.0000545

EpiControl AF: 0.000178

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:21 Other:1

Revision: criteria provided, multiple submitters, no conflicts

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	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. -
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	Baylor Genetics	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals	Feb 01, 2019	- -

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	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, 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	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

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. -
Likely pathogenic, no assertion criteria provided	research	NIHR Bioresource Rare Diseases, University of Cambridge	Jan 01, 2015	- -

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

- -

Rare genetic deafness Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jul 05, 2017

The p.Asn48Lys variant in CLRN1 is known to be pathogenic (Adato 2002, Fields 20 02, Ness 2003). It has been identified in 0.5% (53/9850) of Ashkenazi Jewish chr omosomes including 1 homozygote by the Genome Aggregation Database (gnomAD, http ://gnomad.broadinstitute.org; dbSNP rs111033258). This variant is common in the Ashkenazi Jewish population and it is thought to be a founder mutation. In summ ary, this variant meets criteria to be classified as pathogenic for Usher syndro me type III in an autosomal recessive manner. -

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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.87
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	15
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.72	D;.;.
Eigen	Benign	0.0061
Eigen_PC	Benign	-0.16
FATHMM_MKL	Benign	0.67	D
LIST_S2	Uncertain	0.89	D;D;D
M_CAP	Uncertain	0.14	D
MetaRNN	Benign	0.023	T;T;T
MetaSVM	Uncertain	-0.10	T
MutationAssessor	Uncertain	2.4	M;M;.
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-3.0	D;D;.
REVEL	Uncertain	0.52
Sift	Pathogenic	0.0	D;D;.
Sift4G	Pathogenic	0.0	D;D;.
Polyphen		1.0	D;.;.
Vest4		0.92
MutPred		0.76		Loss of sheet (P = 3e-04);Loss of sheet (P = 3e-04);.;
MVP		0.74
MPC		0.19
ClinPred		0.18	T
GERP RS		-5.2
Varity_R		0.75
gMVP		0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs111033258; hg19: chr3-150690352;