3-184036084-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_001145143.1(HTR3D):​c.181G>A​(p.Val61Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,551,436 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.00097 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 1 hom. )

Consequence

HTR3D
NM_001145143.1 missense

Scores

18

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.877
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 -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0074207485).
BP6
Variant 3-184036084-G-A is Benign according to our data. Variant chr3-184036084-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3107554.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HTR3DNM_001145143.1 linkuse as main transcriptc.181G>A p.Val61Ile missense_variant 3/8 ENST00000428798.7 NP_001138615.1 Q70Z44-4
HTR3DNM_001163646.2 linkuse as main transcriptc.364G>A p.Val122Ile missense_variant 3/8 NP_001157118.1 Q70Z44-1
HTR3DNM_182537.3 linkuse as main transcriptc.-31-285G>A intron_variant NP_872343.2 Q70Z44F6WC43
HTR3DNM_001410851.1 linkuse as main transcriptc.3+862G>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.181G>A p.Val61Ile missense_variant 3/85 NM_001145143.1 ENSP00000405409.2 Q70Z44-4
HTR3DENST00000382489.3 linkuse as main transcriptc.364G>A p.Val122Ile missense_variant 3/81 ENSP00000371929.3 Q70Z44-1
HTR3DENST00000334128.6 linkuse as main transcriptc.-31-285G>A intron_variant 1 ENSP00000334315.2 F6WC43
HTR3DENST00000453435.1 linkuse as main transcriptc.3+862G>A intron_variant 1 ENSP00000389268.1 Q70Z44-3

Frequencies

GnomAD3 genomes
AF:
0.000973
AC:
148
AN:
152184
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000338
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00176
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000824
AC:
129
AN:
156468
Hom.:
0
AF XY:
0.000785
AC XY:
65
AN XY:
82854
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000693
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000237
Gnomad NFE exome
AF:
0.00175
Gnomad OTH exome
AF:
0.000455
GnomAD4 exome
AF:
0.00149
AC:
2078
AN:
1399134
Hom.:
1
Cov.:
32
AF XY:
0.00146
AC XY:
1008
AN XY:
690100
show subpopulations
Gnomad4 AFR exome
AF:
0.000222
Gnomad4 AMR exome
AF:
0.000674
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000126
Gnomad4 FIN exome
AF:
0.000406
Gnomad4 NFE exome
AF:
0.00181
Gnomad4 OTH exome
AF:
0.00126
GnomAD4 genome
AF:
0.000972
AC:
148
AN:
152302
Hom.:
0
Cov.:
32
AF XY:
0.000900
AC XY:
67
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.000337
Gnomad4 AMR
AF:
0.000719
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.00176
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.00132
Hom.:
1
Bravo
AF:
0.000888
TwinsUK
AF:
0.00135
AC:
5
ALSPAC
AF:
0.00234
AC:
9
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.00189
AC:
6
ExAC
AF:
0.000325
AC:
9
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsAug 30, 2021This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.081
BayesDel_addAF
Benign
-0.51
T
BayesDel_noAF
Benign
-0.52
CADD
Benign
0.83
DANN
Benign
0.22
DEOGEN2
Benign
0.040
.;T
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.075
N
LIST_S2
Benign
0.55
T;T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.0074
T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
-1.6
.;N
PROVEAN
Benign
0.66
N;N
REVEL
Benign
0.10
Sift
Benign
1.0
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.015
.;B
Vest4
0.15
MVP
0.20
MPC
0.13
ClinPred
0.035
T
GERP RS
-1.2
Varity_R
0.023
gMVP
0.019

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs188854019; hg19: chr3-183753872; API