GeneBe

rs71047866

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001135091.2(MUC15):​c.*1212_*1229delGTGTGTGTGTGTGTGTGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000423 in 661,844 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000042 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000042 ( 0 hom. )

Consequence

MUC15
NM_001135091.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.701
Variant links:
Genes affected
MUC15 (HGNC:14956): (mucin 15, cell surface associated) Predicted to be located in Golgi lumen and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MUC15NM_001135091.2 linkc.*1212_*1229delGTGTGTGTGTGTGTGTGT 3_prime_UTR_variant Exon 5 of 5 ENST00000529533.6 NP_001128563.1 Q8N387A0A0A0MT67
ANO3NM_031418.4 linkc.1447+79_1447+96delACACACACACACACACAC intron_variant Intron 14 of 26 ENST00000256737.8 NP_113606.2 Q9BYT9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MUC15ENST00000529533 linkc.*1212_*1229delGTGTGTGTGTGTGTGTGT 3_prime_UTR_variant Exon 5 of 5 1 NM_001135091.2 ENSP00000431983.1 A0A0A0MT67
ANO3ENST00000256737.8 linkc.1447+79_1447+96delACACACACACACACACAC intron_variant Intron 14 of 26 1 NM_031418.4 ENSP00000256737.3 Q9BYT9-1

Frequencies

GnomAD3 genomes
AF:
0.0000417
AC:
6
AN:
144008
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000782
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000451
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000152
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000425
AC:
22
AN:
517836
Hom.:
0
AF XY:
0.0000462
AC XY:
13
AN XY:
281644
show subpopulations
Gnomad4 AFR exome
AF:
0.000127
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000383
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000560
Gnomad4 OTH exome
AF:
0.0000374
GnomAD4 genome
AF:
0.0000417
AC:
6
AN:
144008
Hom.:
0
Cov.:
0
AF XY:
0.0000430
AC XY:
3
AN XY:
69830
show subpopulations
Gnomad4 AFR
AF:
0.0000782
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000451
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000152
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs71047866; hg19: chr11-26581382; API