Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_004004.5(GJB2):c.571T>C (p.Phe191Leu)

CA134989

44760 (ClinVar)

Gene: GJB2

Condition: nonsyndromic genetic deafness

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 3d336d40-28c9-4f51-b57c-d5a224b55959

HGVS expressions

NM_004004.5:c.571T>C

NM_004004.5(GJB2):c.571T>C (p.Phe191Leu)

NC_000013.11:g.20189011A>G

CM000675.2:g.20189011A>G

NC_000013.10:g.20763150A>G

CM000675.1:g.20763150A>G

NC_000013.9:g.19661150A>G

NG_008358.1:g.8965T>C

NM_004004.6:c.571T>C

ENST00000382844.1:c.571T>C

ENST00000382848.4:c.571T>C

Uncertain Significance

BS2 PM3_Supporting PP3 PS3_Supporting BS1_Supporting

PS4

Evidence Links 18

Expert Panel

Hearing Loss VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Hearing Loss VCEP

The c.571T>C (p.Phe191Leu) variant in GJB2 has been reported in over 19 Asian probands in the literature. However, a case control comparison using Chi-squared analysis did not show a statistical significance between cases and controls in the published studies, or between cases and East Asians in gnomAD (case chromosomes= 19/16415, control chromosomes = 6/8626, 36/18870 East Asian chromosomes in gnomAD; PMIDs 19366456, 15700112, 23826813, 27247933, 27792752, 12792423, 12560944, 19043807, 27627659, 20497192 and https://doi.org/10.1016/S1672-2930(07)50004-8). The filtering allele frequency of the p.Phe191Leu variant in the GJB2 gene is 0.14% for East Asian chromosomes in gnomAD (36/18870 with 95% CI), which is a higher frequency than would be expected for an autosomal recessive pathogenic variant based on the thresholds defined by the ClinGen Hearing Loss Expert Panel (BS1_Supporting). This variant has been detected in 1 individual with hearing loss who was homozygous for the variant, and in 4 compound heterozygous individuals who had a second pathogenic GJB2 variant identified (3 with p.Val37Ile and 1 with c.235delC) (Oguchi 2005 PMID: 15700112; ARUP SCV000603821; Partners Lab for Molecular Medicine SCV000061527). Phase was not confirmed for any of these individuals. It is possible that these homozygous and compound heterozygous observations are due to the relatively high allele frequencies of these variants in gnomAD and therefore PM3 was downgraded (PM3_Supporting). In addition, this variant was reported in the homozygous state in a normal hearing parent (BS2, Wattanasirichiagoon 2004, PMID 15479191). Computational prediction analysis using REVEL suggests that the variant may impact the protein (PP3). Two in vitro functional studies demonstrates that this variant resulted in abnormal protein trafficking and retention of the protein in the endoplasmic reticulum; however, further electrical coupling studies were not performed (PS3_Supporting; PMID: 23967136, 26749107). In summary, due to conflicting evidence, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BS1_Supporting, BS2, PM3_Supporting, PS3_Supporting, PP3.

BS2

Identified in normal hearing parent in the homozygous state (Wattanasirichiagoon, 2004)

F191L identified via sequencing, but categorized as non pathogenic because it was identified in homozygous state in hearing father of an individual with hearing loss. Was not identified in any of the 410 Thai control chromosomes included in study. Study included 166 unrelated Thai individuals with hearing loss. PubMed:15479191

PM3_Supporting

Total of 2.5 points. 2 points internal data (LMM + ARUP), 0.5 points homozygous case (Oguchi_2005_15700112). No points scored for proband with V198Met from Dai_2009_19366456 because phase unknown, VUS on remaining allele, Not categorized in ClinVar, 3 papers in HGMD entry, absent from gnomAD, phase unknown, could do variant assessment.

60 unrelated Japanese probands underwent GJB2 sequencing. 1 individual homozygous for Phe191Leu identified with mild sloping to profound SNHL. PM3 = 0.5 POINTS. 147 unrelated Japanese hearing controls. Variant not found. PubMed:15700112

PP3

Computational prediction analysis using REVEL suggests that the variant may impact the protein

PS3_Supporting

2 studies performed in HeLa cells revealed that F191L mutants were not properly trafficked to the plasma membrane, with immunocytochemsistyr / fluorescence showing retention in the ER and aggregation in the cytoplasm.

Phe191 is in transmembrane domain and forms hydrophobic interaction core with other residues. This core is thought to contribute to stabilization of molecule. Therefore, it is assumed that a mutation at this residue would destabilize intramolecular interactions. HeLA cells transfected with F191L construct. transported to the cell membrane, and, using immunocytochemistry confirmed that they stayed in the cytoplasm, particularly in the ER (Supplementary material Fig. S1), potentially as a result of the loss of the ability to form GJs. PubMed:26749107

Bioinformatic analysis of GJB2 missense variants (already scored PP3) PubMed:25388846

When expressed in HeLa cells, F191L showed intracellular fluorescence with patterns indicating ER retention or cytoplasmic aggregation. F191L mutant formed large aggregates with possible plasma membrane locations, but closer inspection of the images showed that the fluorescence patterns did not have appearance of gap junctions, since apposing plasma membranes did not appear close enough together to make a gap junction. Computational modeling: Phe191 side chain is buried in the 4-helix bundle and makes hydrophobic interactions with Arg75 (alpha-helix transmembrane domain 2, TM2), Leu79 (TM2) from an adjacent monomer as well as amino acids Val38 (TM1), Ala39 (TM1) and Val190 (TM4) from the same monomer. Possible effect: substitution of Leu would destabilize structure by causing formation of hydrophobic cavity. PubMed:23967136

BS1_Supporting

0.191% (36/18870) of East Asian chromosomes in gnomAD. Filtering allele frequency : 0.14%. This meets BS1_Supporting for AR.

Blood samples were obtained from 2,072 Korean newborns with normal hearing, and underwent sequencing of GJB2 2 heterozygotes with Phe191Leu identified. PubMed:19043807

Study performed in cohort of Australian school children, performed hearing tests, and sequenced 48 children with mild hearing loss for GJB2. Each child with hearing loss was matched with controls with normal hearing. Total of 90 controls sequenced. Identified variant in 1/180 control chromosomes. Study reports characteristics of control cohort ( Ethnic breakdown: 9 Asians, 1 Black, 62 white, 17 more than 1 race, 1 not reported) , but does not say if this control was Asian. PubMed:16840571

PS4

There was no statistical significance between the number of cases versus controls by a Chi squared analysis with Yates correction. This comparison was done by comparing the cases and controls from the below publications and comparing cases from the same publications and the East Asian alleles in gnomAD (36/18870) Dai_2009_19366456 Ming-Kun_2007_NO PMID Oguchi_2005_15700112 Wei_2013_23826813 Zheng_2016_27247933 Gao_2016_27792752 Hwa_2003_12792423 Ohtsuka_2003_12560944 hHan_2008_19043807 Mori_2016_27627659 Tsukada_2010_20497192

An unselected cohort of 509 healthy Japanese individuals were sequenced for GJB2 to determine carrier frequencies. 56/509 subjects had subjectively experienced hearing difficulties Phe191leu was found in 1 heterozygote. 0.1% (1/1018) Japanese alleles. PubMed:26178431

There were 324 Taiwanese patients with nonsyndromic prelingual hearing loss and 432 Taiwanese subjects with apparently normal hearing. Phe191Leu identified in 3/648 affected chromosomes. In each of these individuals, a 2nd mutation was not found. Phe191Leu was present in in 1/864 controls chromosomes. PubMed:12792423

1511 Japanese probands with hearing loss. 252 unrelated Japanese controls. F191L was identified in 1/504 control chromosomes. PubMed:20497192

658 unrelated patients with SNHL from China (Han) were sequenced for GJB2. 462 normal hearing controls were also included. F191L identified in 4/658 patients with HL, all 4 were hets only (allele freq 0.3%, 4/1316). Was not identified in controls. PubMed:23826813

DID NOT USE FOR CASE CONTROL COMPARISON. 2398 Chinese individuals with SNHL were sequenced for GJB2. 1057 control individuals matched for region and ethnicity. F191L identified, described as polymorphism but was not further commented on, PubMed:24256046

Blood samples were obtained from 2,072 Korean newborns with normal hearing, and underwent sequencing of GJB2. 2 heterozygotes with Phe191Leu identified. PubMed:19043807

Phe191Leu is at similar frequency in patients vs. controls. 1227 unrelated Japanese individuals with SNHL underwent GJB2 sequencing. Phe191Leu identified in 4/2454 HL alleles. However, these individuals were all heterozygous, without a second variant identified. 147 unrelated Japanese controls. 1/294 control chromosomes harbored Phe191Leu PubMed:12560944

339 patients with HL from Linyi (city in Shandong province, China) underwent SNP arrays designed to capture 115 mutations in GJB2, SLC26A4, and MTRNR1. Phe191Leu identified in 3 patients, 2nd mutation was not identified in any (3/678, 0.44%). PubMed:27247933

717 unrelated Japanese patients with hearing loss were screened for a list of 154 mutations using genotyping and NGS sequencing. No patients were found to harbor mutation, but it was identified in 0.19% (1/538) control chromosomes PubMed:27627659

695 Chinese patients recruited and underwent screening using a SNP chip to identify a set list of variants in GJB2, SLC, MTRNR1. 2 patients were heterozygous for the Phe191Leu variant (Allele frequency in cases 0.14% (2/1390). Authors show that the allele frequency in their patient cohort is not higher than in East Asian in exac (0.2%), or in 1000 Genomes (0.49% Han Chinese). PubMed:27792752

2063 unrelated Chinese patients with hearing loss were sequenced for GJB2. 301 Han control individuals also included. 1 patient with F191L, V198Met (not categorized in ClinVar, 3 papers in HGMD entry, absent from gnomAD) and V27I (benign) was identified in the study. (no points for PM3, phase WAS NOT determined). PubMed:19366456

51 probands (76 individuals) with hearing loss from different regions in Russia (Altaians, n= 40; Russians, n = 17; Kazakhs, n = 3; mixed or other ethnicity, n = 16) 130 unrelated subjects of Altaian origin with no familial history of hearing problems were used as controls. Phe191Leu was identified in 0.4% (1/260) of controls chromosomes PubMed:15790391

study performed in cohort of Australian school children, performed hearing tests, and sequenced 48 children with mild hearing loss for GJB2. Each child with hearing loss was matched with controls with normal hearing. Identified variant in 1/180 control chromosomes. Study reports characteristics of control cohort ( Ethnic breakdown: 9 Asians, 1 Black, 62 white, 17 more than 1 race, 1 not reported) , but does not say if this control was Asian. PubMed:16840571

Approved on: 2018-09-24

Published on: 2019-07-17

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