chr11-26639153-A-G

Variant names:

• chr11-26639153-A-G
• rs587776923
• NM_031418.4:c.2053A>G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The NM_031418.4(ANO3):​c.2053A>G​(p.Ser685Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ANO3 NM_031418.4 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 9.32

Genes affected

ANO3 (HGNC:14004): (anoctamin 3) The protein encoded by this gene belongs to the TMEM16 family of predicted membrane proteins, that are also known as anoctamins. While little is known about the function of this gene, mutations in this gene have been associated with some cases of autosomal dominant craniocervical dystonia. Cells from individuals with a mutation in this gene exhibited abnormalities in endoplasmic reticulum-dependent calcium signaling. Studies in rat show that the rat ortholog of this protein interacts with, and modulates the activity of a sodium-activated potassium channel. Deletion of this gene caused increased pain sensitivity in the rat model system. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-26639153-A-G is Pathogenic according to our data. Variant chr11-26639153-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 39498.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANO3	NM_031418.4	c.2053A>G	p.Ser685Gly	missense_variant	Exon 21 of 27	ENST00000256737.8	NP_113606.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANO3	ENST00000256737.8	c.2053A>G	p.Ser685Gly	missense_variant	Exon 21 of 27	1	NM_031418.4	ENSP00000256737.3
ANO3	ENST00000672621.1	c.2236A>G	p.Ser746Gly	missense_variant	Exon 22 of 28			ENSP00000500506.1
ANO3	ENST00000525139.5	c.2005A>G	p.Ser669Gly	missense_variant	Exon 21 of 27	5		ENSP00000432576.1
ANO3	ENST00000531568.1	c.1615A>G	p.Ser539Gly	missense_variant	Exon 18 of 24	2		ENSP00000432394.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Dystonia 24 Pathogenic:1

Dec 07, 2012

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.37
BayesDel_addAF	Uncertain	0.082	D
BayesDel_noAF	Benign	-0.12
CADD	Pathogenic	27
DANN	Benign	0.66
DEOGEN2	Benign	0.076	T;T;.
Eigen	Benign	0.15
Eigen_PC	Uncertain	0.25
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.91	D;D;D
M_CAP	Benign	0.051	D
MetaRNN	Uncertain	0.48	T;T;T
MetaSVM	Benign	-0.69	T
MutationAssessor	Benign	0.29	.;N;.
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	0.39	N;N;N
REVEL	Uncertain	0.40
Sift	Benign	1.0	T;T;T
Sift4G	Benign	1.0	T;T;T
Polyphen		1.0	.;D;.
Vest4		0.65
MutPred		0.39		.;Loss of glycosylation at S685 (P = 0.0577);.;
MVP		0.65
MPC		1.7
ClinPred		0.74	D
GERP RS		5.8
Varity_R		0.28
gMVP		0.96

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: rs587776923; hg19: chr11-26660700;