rs6443930

Variant names:

• chr3-184036506-G-A
• rs6443930
• NM_001145143.1:c.329G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-184036506-G-A
• chr3-184036506-G-C
• chr3-184036506-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001145143.1(HTR3D):​c.329G>A​(p.Gly110Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: HTR3D NM_001145143.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657
• Publications: 45 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.1).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR3D	NM_001145143.1	c.329G>A	p.Gly110Asp	missense_variant	Exon 4 of 8	ENST00000428798.7	NP_001138615.1
HTR3D	NM_182537.3	c.107G>A	p.Gly36Asp	missense_variant	Exon 3 of 6		NP_872343.2
HTR3D	NM_001163646.2	c.511+1G>A		splice_donor_variant, intron_variant	Intron 4 of 7		NP_001157118.1
HTR3D	NM_001410851.1	c.3+1284G>A		intron_variant	Intron 2 of 4		NP_001397780.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR3D	ENST00000428798.7	c.329G>A	p.Gly110Asp	missense_variant	Exon 4 of 8	5	NM_001145143.1	ENSP00000405409.2
HTR3D	ENST00000334128.6	c.107G>A	p.Gly36Asp	missense_variant	Exon 3 of 6	1		ENSP00000334315.2
HTR3D	ENST00000382489.3	c.511+1G>A		splice_donor_variant, intron_variant	Intron 4 of 7	1		ENSP00000371929.3
HTR3D	ENST00000453435.1	c.3+1284G>A		intron_variant	Intron 1 of 3	1		ENSP00000389268.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 59

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 4212

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.095
BayesDel_addAF	Uncertain	0.088	D
BayesDel_noAF	Benign	-0.49
CADD	Benign	13
DANN	Benign	0.97
Eigen	Benign	-0.29
Eigen_PC	Benign	-0.37
FATHMM_MKL	Benign	0.73	D
M_CAP	Benign	0.024	T
PhyloP100		0.66
ClinPred		0.23	T
GERP RS		4.1
Mutation Taster		=23/77	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6443930; hg19: chr3-183754294;