NM_000166.6:c.644G>A

Variant names:

• chrX-71224351-G-A
• rs864622215
• NM_000166.6:c.644G>A

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 6P and 5B. PM1 PM5 PP2 PP5 BP4 BS2

The NM_000166.6(GJB1):​c.644G>A​(p.Arg215Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000073 in 1,096,602 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R215W) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 0.0000073 (0 hom. 6 hem.)
• Consequence: GJB1 NM_000166.6 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1
• Conservation: PhyloP100: 2.70
• Publications: 8 publications found

Genes affected

GJB1 (HGNC:4283): (gap junction protein beta 1) This gene encodes a member of the gap junction protein family. The gap junction proteins are membrane-spanning proteins that assemble to form gap junction channels that facilitate the transfer of ions and small molecules between cells. According to sequence similarities at the nucleotide and amino acid levels, the gap junction proteins are divided into two categories, alpha and beta. Mutations in this gene cause X-linked Charcot-Marie-Tooth disease, an inherited peripheral neuropathy. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Oct 2008]

GJB1 Gene-Disease associations (from GenCC):

• Charcot-Marie-Tooth disease X-linked dominant 1

  Inheritance: XL Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia, ClinGen, Labcorp Genetics (formerly Invitae)
• X-linked progressive cerebellar ataxia

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 14 uncertain in NM_000166.6
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrX-71224350-C-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 246098.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 135 curated pathogenic missense variants (we use a threshold of 10). The gene has 4 curated benign missense variants. Trascript score misZ: NaN (below the threshold of 3.09). GenCC associations: The gene is linked to Charcot-Marie-Tooth disease X-linked dominant 1, X-linked progressive cerebellar ataxia.
• PP5: Variant X-71224351-G-A is Pathogenic according to our data. Variant chrX-71224351-G-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 1958026.
• BP4: Computational evidence support a benign effect (MetaRNN=0.3405183). . Strength limited to SUPPORTING due to the PP5.
• BS2: High Hemizygotes in GnomAdExome4 at 6 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJB1	NM_000166.6	c.644G>A	p.Arg215Gln	missense_variant	Exon 2 of 2	ENST00000361726.7	NP_000157.1
GJB1	NM_001097642.3	c.644G>A	p.Arg215Gln	missense_variant	Exon 2 of 2		NP_001091111.1
GJB1	NM_001440770.1	c.644G>A	p.Arg215Gln	missense_variant	Exon 3 of 3		NP_001427699.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GJB1	ENST00000361726.7	c.644G>A	p.Arg215Gln	missense_variant	Exon 2 of 2	1	NM_000166.6	ENSP00000354900.6

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome AF: 0.00000730 AC: 8 AN: 1096602 Hom.: 0 Cov.: 32 AF XY: 0.0000166 AC XY: 6 AN XY: 362294

African (AFR) AF: 0.00 AC: 0 AN: 26392

American (AMR) AF: 0.00 AC: 0 AN: 35183

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19355

East Asian (EAS) AF: 0.00 AC: 0 AN: 30195

South Asian (SAS) AF: 0.000129 AC: 7 AN: 54059

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39387

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4134

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 841829

Other (OTH) AF: 0.0000217 AC: 1 AN: 46068

GnomAD4 genome Cov.: 22

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Charcot-Marie-Tooth disease X-linked dominant 1 Pathogenic:1

May 30, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: GJB1 c.644G>A (p.Arg215Gln) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 179956 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.644G>A in individuals affected with Charcot-Marie-Tooth disease X-linked dominant 1 has been reported. A different variant affecting the same codon has been classified as pathogenic by our lab (c.643C>T, p.Arg215Trp), supporting the critical relevance of codon 215 to GJB1 protein function. In an in vitro functional system using Xenopus oocytes, the variant was shown not to form gap junctions leading to a complete loss of function (Castro_1999). The following publication has been ascertained in the context of this evaluation (PMID: 10234007). ClinVar contains an entry for this variant (Variation ID: 1958026). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Charcot-Marie-Tooth Neuropathy X Uncertain:1

Mar 25, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 215 of the GJB1 protein (p.Arg215Gln). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GJB1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Experimental studies have shown that this missense change affects GJB1 function (PMID: 10234007). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant disrupts the p.Arg215 amino acid residue in GJB1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8162049, 8816997, 9187667, 22464564). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Uncertain	0.056	T
BayesDel_noAF	Benign	-0.16
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.37	T;T;T;T;T
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.81	.;.;.;.;T
M_CAP	Pathogenic	0.87	D
MetaRNN	Benign	0.34	T;T;T;T;T
MetaSVM	Uncertain	0.44	D
MutationAssessor	Benign	0.63	N;N;N;N;N
PhyloP100		2.7
PrimateAI	Uncertain	0.52	T
PROVEAN	Benign	-0.86	N;.;N;.;N
REVEL	Uncertain	0.36
Sift	Benign	0.044	D;.;D;.;D
Sift4G	Uncertain	0.060	T;.;T;.;T
Polyphen		0.058	B;B;B;B;B
Vest4		0.13
MutPred		0.57		Loss of MoRF binding (P = 0.0237);Loss of MoRF binding (P = 0.0237);Loss of MoRF binding (P = 0.0237);Loss of MoRF binding (P = 0.0237);Loss of MoRF binding (P = 0.0237);
MVP		0.91
MPC		0.89
ClinPred		0.80	D
GERP RS		4.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.29
gMVP		0.97
Mutation Taster		=55/45	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs864622215; hg19: chrX-70444201;