chr11-61958282-A-G

Position:

• chr11-61958282-A-G

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2 PP3_Strong PP5_Very_Strong

The NM_001363593.2(BEST1):​c.-325A>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: BEST1 NM_001363593.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:5 U:1
• Conservation: PhyloP100: 9.09

Genes affected

BEST1 (HGNC:12703): (bestrophin 1) This gene encodes a member of the bestrophin gene family. This small gene family is characterized by proteins with a highly conserved N-terminus with four to six transmembrane domains. Bestrophins may form chloride ion channels or may regulate voltage-gated L-type calcium-ion channels. Bestrophins are generally believed to form calcium-activated chloride-ion channels in epithelial cells but they have also been shown to be highly permeable to bicarbonate ion transport in retinal tissue. Mutations in this gene are responsible for juvenile-onset vitelliform macular dystrophy (VMD2), also known as Best macular dystrophy, in addition to adult-onset vitelliform macular dystrophy (AVMD) and other retinopathies. Alternative splicing results in multiple variants encoding distinct isoforms.[provided by RefSeq, Nov 2008]

BEST1 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.975
• PP5: Variant 11-61958282-A-G is Pathogenic according to our data. Variant chr11-61958282-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 166746.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-61958282-A-G is described in Lovd as [Pathogenic]. Variant chr11-61958282-A-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BEST1	NM_004183.4	c.851A>G	p.Tyr284Cys	missense_variant	7/11	ENST00000378043.9	NP_004174.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BEST1	ENST00000378043.9	c.851A>G	p.Tyr284Cys	missense_variant	7/11	1	NM_004183.4	ENSP00000367282.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:5 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2 Uncertain:1

Uncertain significance, flagged submission	clinical testing	Eurofins Ntd Llc (ga)	Apr 16, 2014	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 13, 2023	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 35754583, 33090715, 21109774, 35973442, 32207364) -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 18, 2024	This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 284 of the BEST1 protein (p.Tyr284Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with autosomal dominant BEST1-related conditions (PMID: 21109774, 32207364; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 166746). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt BEST1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. -

Vitelliform macular dystrophy 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University of Leipzig Medical Center

Jan 01, 2019

- -

BEST1-related disorder Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 22, 2024

The BEST1 c.851A>G variant is predicted to result in the amino acid substitution p.Tyr284Cys. This variant has been reported in the heterozygous state in individuals with BEST1-related disease (Table S4, Liu et al. 2020. PubMed ID: 33090715; Garza-Garza et al. 2020. PubMed ID: 32207364; Hoyek et al. 2022. PubMed ID: 35754583; Supplementary Table 1 Wang et al. 2022. PubMed ID: 35973442; zygosity unknown in Cohn et al. 2010. PubMed ID: 21109774). In two families, this variant was inherited from affected or mildly affected parents, suggesting variable expressivity and/or incomplete penetrance, and also identified in an affected sibling (Garza-Garza et al. 2020. PubMed ID: 32207364; Hoyek et al. 2022. PubMed ID: 35754583). This variant is interpreted as likely pathogenic or pathogenic by multiple submitters in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/166746/). This variant has not been reported in a large population database, indicating it is rare. This variant is interpreted as likely pathogenic. -

Stargardt disease Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Department of Genetics, Fundacion Jimenez Diaz University Hospital

-

Variant not found in gnomAD. Same amino acid change previously reported pathogenic (ClinVar: VCV000813024.1, predicted deleterious by in-silico pathogenicity predictors. (ACMG: PS2 Strong; PM2 Moderate; PP3 Supporting) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.71
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.59
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.98	D;.;D
Eigen	Pathogenic	0.78
Eigen_PC	Uncertain	0.66
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.99	D;D;D
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.97	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.7	H;.;.
PrimateAI	Uncertain	0.73	T
PROVEAN	Pathogenic	-8.8	D;D;D
REVEL	Pathogenic	0.98
Sift	Pathogenic	0.0	D;D;D
Sift4G	Pathogenic	0.0	D;D;D
Polyphen		1.0	D;D;D
Vest4		0.98
MutPred		0.77		Loss of catalytic residue at L279 (P = 0.096);.;.;
MVP		0.99
MPC		1.0
ClinPred		1.0	D
GERP RS		4.9
Varity_R		0.87
gMVP		0.97

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

Publications

LitVar

Other links and lift over

dbSNP: rs727503824; hg19: chr11-61725754;