rs139765369
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_001088.3(AANAT):āc.92C>Gā(p.Thr31Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,258 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: not found (cov: 32)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
AANAT
NM_001088.3 missense
NM_001088.3 missense
Scores
5
11
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.34
Genes affected
AANAT (HGNC:19): (aralkylamine N-acetyltransferase) The protein encoded by this gene belongs to the acetyltransferase superfamily. It is the penultimate enzyme in melatonin synthesis and controls the night/day rhythm in melatonin production in the vertebrate pineal gland. Melatonin is essential for the function of the circadian clock that influences activity and sleep. This enzyme is regulated by cAMP-dependent phosphorylation that promotes its interaction with 14-3-3 proteins and thus protects the enzyme against proteasomal degradation. This gene may contribute to numerous genetic diseases such as delayed sleep phase syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM1
In a modified_residue Phosphothreonine; by PKA (size 0) in uniprot entity SNAT_HUMAN
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AANAT | NM_001088.3 | c.92C>G | p.Thr31Arg | missense_variant | Exon 2 of 4 | ENST00000392492.8 | NP_001079.1 | |
AANAT | NM_001166579.2 | c.227C>G | p.Thr76Arg | missense_variant | Exon 5 of 7 | NP_001160051.1 | ||
AANAT | NR_110548.2 | n.292C>G | non_coding_transcript_exon_variant | Exon 2 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AANAT | ENST00000392492.8 | c.92C>G | p.Thr31Arg | missense_variant | Exon 2 of 4 | 1 | NM_001088.3 | ENSP00000376282.2 | ||
AANAT | ENST00000250615.7 | c.227C>G | p.Thr76Arg | missense_variant | Exon 5 of 7 | 1 | ENSP00000250615.2 | |||
AANAT | ENST00000585649.1 | c.206C>G | p.Thr69Arg | missense_variant | Exon 1 of 3 | 1 | ENSP00000468717.1 | |||
AANAT | ENST00000587798.1 | n.92C>G | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 | ENSP00000468239.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461258Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726976
GnomAD4 exome
AF:
AC:
1
AN:
1461258
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
726976
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T;.
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
.;M;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.
REVEL
Uncertain
Sift
Pathogenic
D;D;.
Sift4G
Pathogenic
D;D;D
Polyphen
1.0
.;D;.
Vest4
MutPred
0.23
.;Loss of phosphorylation at T31 (P = 0.0073);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.