3-184036382-C-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001145143.1(HTR3D):​c.205C>A​(p.Gln69Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

HTR3D
NM_001145143.1 missense

Scores

18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.849
Variant links:
Genes affected
HTR3D (HGNC:24004): (5-hydroxytryptamine receptor 3D) The protein encoded this gene belongs to the ligand-gated ion channel receptor superfamily. This gene encodes subunit D of the type 3 receptor for 5-hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a mitogen and a hormone. This hormone has been linked to neuropsychiatric disorders, including anxiety, depression, and migraine. Serotonin receptors causes fast and depolarizing responses in neurons following activation. The genes encoding subunits C, D and E of this type 3 receptor form a cluster on chromosome 3. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0468733).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HTR3DNM_001145143.1 linkuse as main transcriptc.205C>A p.Gln69Lys missense_variant 4/8 ENST00000428798.7 NP_001138615.1 Q70Z44-4
HTR3DNM_001163646.2 linkuse as main transcriptc.388C>A p.Gln130Lys missense_variant 4/8 NP_001157118.1 Q70Z44-1
HTR3DNM_182537.3 linkuse as main transcriptc.-18C>A 5_prime_UTR_variant 3/6 NP_872343.2 Q70Z44F6WC43
HTR3DNM_001410851.1 linkuse as main transcriptc.3+1160C>A intron_variant NP_001397780.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HTR3DENST00000428798.7 linkuse as main transcriptc.205C>A p.Gln69Lys missense_variant 4/85 NM_001145143.1 ENSP00000405409.2 Q70Z44-4
HTR3DENST00000382489.3 linkuse as main transcriptc.388C>A p.Gln130Lys missense_variant 4/81 ENSP00000371929.3 Q70Z44-1
HTR3DENST00000334128.6 linkuse as main transcriptc.-18C>A 5_prime_UTR_variant 3/61 ENSP00000334315.2 F6WC43
HTR3DENST00000453435.1 linkuse as main transcriptc.3+1160C>A intron_variant 1 ENSP00000389268.1 Q70Z44-3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000796
AC:
2
AN:
251334
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135818
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461796
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
727186
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsSep 09, 2021The c.388C>A (p.Q130K) alteration is located in exon 4 (coding exon 4) of the HTR3D gene. This alteration results from a C to A substitution at nucleotide position 388, causing the glutamine (Q) at amino acid position 130 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.083
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
1.5
DANN
Benign
0.67
DEOGEN2
Benign
0.025
.;T
Eigen
Benign
-1.0
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.019
N
LIST_S2
Benign
0.47
T;T
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.047
T;T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
0.31
.;N
PROVEAN
Benign
0.37
N;N
REVEL
Benign
0.16
Sift
Benign
1.0
T;T
Sift4G
Benign
0.64
T;T
Polyphen
0.0090
.;B
Vest4
0.22
MutPred
0.46
.;Gain of ubiquitination at Q130 (P = 0.0117);
MVP
0.45
MPC
0.21
ClinPred
0.029
T
GERP RS
0.15
Varity_R
0.14
gMVP
0.072

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.12
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: rs1364533857; hg19: chr3-183754170; API