rs10985760
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_001004453.3(OR1L6):c.644T>A(p.Ile215Asn) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 16)
Exomes 𝑓: 0.0000035 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
OR1L6
NM_001004453.3 missense
NM_001004453.3 missense
Scores
5
5
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.83
Genes affected
OR1L6 (HGNC:8218): (olfactory receptor family 1 subfamily L member 6) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.784
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR1L6 | NM_001004453.3 | c.644T>A | p.Ile215Asn | missense_variant | 2/2 | ENST00000304720.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR1L6 | ENST00000304720.3 | c.644T>A | p.Ile215Asn | missense_variant | 2/2 | NM_001004453.3 | P1 | ||
OR1L6 | ENST00000373684.1 | c.752T>A | p.Ile251Asn | missense_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 132690Hom.: 0 Cov.: 16 FAILED QC
GnomAD3 genomes
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000350 AC: 3AN: 856484Hom.: 0 Cov.: 12 AF XY: 0.00000450 AC XY: 2AN XY: 444358
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 132690Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0AN XY: 63178
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D
M_CAP
Benign
T
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Benign
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
1.0
.;D
Vest4
MutPred
0.55
.;Loss of catalytic residue at L256 (P = 0.0396);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at