chr9-133636712-T-C

Variant names:

• chr9-133636712-T-C
• rs74853476
• NM_000787.4:c.339+2T>C

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 14P and 1B. PVS1_Strong PM2 PP5_Very_Strong BS1_Supporting

The NM_000787.4(DBH):​c.339+2T>C variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00151 in 1,600,532 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0010 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0016 (0 hom.)
• Consequence: DBH NM_000787.4 splice_donor, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:13 O:1
• Conservation: PhyloP100: 7.55

Genes affected

DBH (HGNC:2689): (dopamine beta-hydroxylase) The protein encoded by this gene is an oxidoreductase belonging to the copper type II, ascorbate-dependent monooxygenase family. The encoded protein, expressed in neuroscretory vesicles and chromaffin granules of the adrenal medulla, catalyzes the conversion of dopamine to norepinephrine, which functions as both a hormone and as the main neurotransmitter of the sympathetic nervous system. The enzyme encoded by this gene exists exists in both soluble and membrane-bound forms, depending on the absence or presence, respectively, of a signal peptide. Mutations in this gene cause dopamine beta-hydroxylate deficiency in human patients, characterized by deficits in autonomic and cardiovascular function, including hypotension and ptosis. Polymorphisms in this gene may play a role in a variety of psychiatric disorders. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 13 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.18770227 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 9-133636712-T-C is Pathogenic according to our data. Variant chr9-133636712-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 1750.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-133636712-T-C is described in Lovd as [Pathogenic]. Variant chr9-133636712-T-C is described in Lovd as [Likely_pathogenic].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.00156 (2256/1448316) while in subpopulation NFE AF= 0.00191 (2127/1111602). AF 95% confidence interval is 0.00185. There are 0 homozygotes in gnomad4_exome. There are 1079 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DBH	NM_000787.4	c.339+2T>C		splice_donor_variant, intron_variant	Intron 1 of 11	ENST00000393056.8	NP_000778.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DBH	ENST00000393056.8	c.339+2T>C		splice_donor_variant, intron_variant	Intron 1 of 11	1	NM_000787.4	ENSP00000376776.2
DBH	ENST00000263611.3	c.333+2T>C		splice_donor_variant, intron_variant	Intron 1 of 2	2		ENSP00000263611.3

Frequencies

GnomAD3 genomes AF: 0.00104 AC: 158 AN: 152100 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000555

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00166

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000722 AC: 172 AN: 238286 Hom.: 0 AF XY: 0.000724 AC XY: 94 AN XY: 129830

Gnomad AFR exome AF: 0.000805

Gnomad AMR exome AF: 0.000435

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000324

Gnomad NFE exome AF: 0.00119

Gnomad OTH exome AF: 0.00149

GnomAD4 exome AF: 0.00156 AC: 2256 AN: 1448316 Hom.: 0 Cov.: 33 AF XY: 0.00150 AC XY: 1079 AN XY: 720860

Gnomad4 AFR exome AF: 0.000418

Gnomad4 AMR exome AF: 0.000403

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000173

Gnomad4 NFE exome AF: 0.00191

Gnomad4 OTH exome AF: 0.00148

GnomAD4 genome AF: 0.00104 AC: 158 AN: 152216 Hom.: 0 Cov.: 32 AF XY: 0.000874 AC XY: 65 AN XY: 74412

Gnomad4 AFR AF: 0.000554

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00166

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.00133 Hom.: 0

Bravo AF: 0.00108

TwinsUK AF: 0.000539 AC: 2

ALSPAC AF: 0.00104 AC: 4

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00128 AC: 11

ExAC AF: 0.000568 AC: 69

EpiCase AF: 0.00125

EpiControl AF: 0.000890

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:13 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Orthostatic hypotension 1 Pathogenic:9 Other:1

Dec 01, 2003

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Sep 30, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The 339+2T>C variant in DBH has been previously reported in 1 homozygous and 5 compound heterozygous individuals with dopamine beta-hydroxylase deficiency and was found to segregate with disease in 2 affected compound heterozygous relatives (Kim 2002, Denium 2004, Kim 2011, ). This variant has been identified in 0.128% (11/8600) of European American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs74853476). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and in vitro splicing assays suggest it causes altered splicing leading to an absent protein (Kim 2011); however, these types of assays may not accurately represent biological function. In summary, this variant meets our criteria to be classified as pathogenic for dopamine beta-hydroxylase deficiency in an autosomal recessive manner (http://pcpgmwww.partners.org/personalizedmedicince/LMM ) based upon segregation studies and functional evidence. -

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects a donor splice site in intron 1 of the DBH gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs74853476, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. Disruption of this splice site has been observed in individuals with dopamine beta-hydroxylase deficiency (PMID: 11857564, 15060114, 21209083, 27778639). It has also been observed to segregate with disease in related individuals. This variant is also known as IVS1+2T>C. ClinVar contains an entry for this variant (Variation ID: 1750). Studies have shown that disruption of this splice site results in abnormal mRNA splicing, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 11857564, 21209083). For these reasons, this variant has been classified as Pathogenic. -

Dec 22, 2023

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 26, 2023

New York Genome Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.339+2T>C variant in DBH has previously been reported in individuals with dopamine beta hydroxylase deficiency [PMID: 11857564, 15060114, 23622564, 27778639], and it has been deposited in ClinVar [ClinVar ID: 1750]. The c.339+2T>C variant is observed in 503 alleles (~0.09% minor allele frequency with 0 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.339+2T>C variant in DBH is located in the canonical splice donor site of exon 1 of this 11 exon gene, and predicted to result in loss of splice donor site [splice AI= 0.5854]. In vitro studies demonstrated the c.339+2T>C (previously IVS1+2T>C) variant results in absent protein [PMID: 21209083]. Based on available evidence this homozygous c.339+2T>C variant identified in DBH is classified as Pathogenic. -

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GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

Common pathogenic variant that causes abnormal splicing [Kim et al 2002, Deinum et al 2004, Kim et al 2011, Phillips et al 2013, Arnold et al 2017] -

Dec 04, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: DBH c.339+2T>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: three predict the variant abolishes a 5' splicing donor site, and one predicts the variant weakens a 5' donor site. At least one publication reports experimental evidence that this variant results in aberrant mRNA splicing leading to the introduction of a premature stop codon (e.g., Kim_2002). The variant allele was found at a frequency of 0.00072 in 238286 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.339+2T>C has been reported in the literature in both homozygous and compound heterozygous individuals affected with Orthostatic Hypotension 1 (e.g., Kim_2002, Deinum_2004). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 15060114, 11857564). Six submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Apr 28, 2017

Illumina Laboratory Services, Illumina

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The DBH c.339+2T>C variant, also referred to as IVS1+2T>C, occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. Across five studies, this variant is reported in a total of 11 dopamine beta-hydroxylas (DBH) deficiency patients, including two homozygotes and nine compound heterozygotes (Kim et al. 2002; Zabetian et al. 2003; Deinum et al. 2004; Kim et al. 2011; Jepma et al. 2011). The variant was also found in a heterozygous state in ten unaffected individuals and family members of patients. The c.339+2T>C variant was reported in a heterozygous state in one of 989 total controls and is reported at a frequency of 0.00128 in the European American population of the Exome Sequencing Project. RT-PCR analysis of the variant mRNA expressed in COS-7 cells showed that the c.339+2T>C variant caused aberrant splicing that resulted in a transcript that included intronic sequence and a premature termination codon (Kim et al. 2002). Additionally, Kim et al. (2011) demonstrated that expression of the c.339+2T>C variant in CHO cells showed no detectable DBH protein. Based on the collective evidence, the c.339+2T>C variant is classified as pathogenic for dopamine beta-hydroxylase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Dec 09, 2020

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 29, 2018

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported as disease-causing [PMID 11857564, 27778639, 21209083] -

not provided Pathogenic:4

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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 05, 2016

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 06, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Published functional studies suggest a damaging effect: non-detectable DBH production (Kim et al., 2011); This variant is associated with the following publications: (PMID: 21209083, 14598346, 31980526, 11857564, 15060114, 21471955, 20301647, 31589614, 27778639) -

-

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Benign	-0.090
CADD	Uncertain	26
DANN	Uncertain	0.99
Eigen	Pathogenic	0.96
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Uncertain	0.96	D
GERP RS		5.2

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.90
SpliceAI score (max)		0.59		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.59		Position offset: -2

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

Publications

LitVar

Other links and lift over

dbSNP: rs74853476; hg19: chr9-136501834;