rs775796002

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001001967.1(OR5D13):​c.242C>A​(p.Pro81His) variant causes a missense 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P81L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

OR5D13
NM_001001967.1 missense

Scores

3
4
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.23
Variant links:
Genes affected
OR5D13 (HGNC:15280): (olfactory receptor family 5 subfamily D member 13) 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jun 2015]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.824

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OR5D13NM_001001967.1 linkc.242C>A p.Pro81His missense_variant Exon 1 of 1 ENST00000623930.1 NP_001001967.1 Q8NGL4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR5D13ENST00000623930.1 linkc.242C>A p.Pro81His missense_variant Exon 1 of 1 6 NM_001001967.1 ENSP00000485428.1 Q8NGL4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.40
BayesDel_addAF
Uncertain
0.057
T
BayesDel_noAF
Benign
-0.16
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.15
T
Eigen
Uncertain
0.39
Eigen_PC
Benign
0.11
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.66
T
M_CAP
Benign
0.011
T
MetaRNN
Pathogenic
0.82
D
MetaSVM
Benign
-1.0
T
MutationAssessor
Pathogenic
4.0
H
PrimateAI
Benign
0.25
T
Polyphen
1.0
D
MutPred
0.62
Gain of ubiquitination at K82 (P = 0.1679);
ClinPred
0.96
D
GERP RS
2.3
Varity_R
0.64
gMVP
0.14

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

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

Other links and lift over

dbSNP: rs775796002; hg19: chr11-55541155; COSMIC: COSV100686779; API