NM_001082971.2(DDC):c.232G>T (p.Ala78Ser) AND Deficiency of aromatic-L-amino-acid decarboxylase

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 17, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001221294.6

Allele description [Variation Report for NM_001082971.2(DDC):c.232G>T (p.Ala78Ser)]

NM_001082971.2(DDC):c.232G>T (p.Ala78Ser)

Genes:

DDC-AS1:DDC antisense RNA 1 [Gene - HGNC]
DDC:dopa decarboxylase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p12.1

Genomic location:

Preferred name:

NM_001082971.2(DDC):c.232G>T (p.Ala78Ser)

HGVS:

NC_000007.14:g.50539998C>A
NG_008742.1:g.30459G>T
NM_000790.4:c.232G>T
NM_001082971.2:c.232G>TMANE SELECT
NM_001242886.2:c.202-2019G>T
NM_001242887.2:c.232G>T
NM_001242888.2:c.201+3887G>T
NM_001242889.2:c.232G>T
NM_001242890.2:c.232G>T
NP_000781.2:p.Ala78Ser
NP_001076440.2:p.Ala78Ser
NP_001229816.2:p.Ala78Ser
NP_001229818.2:p.Ala78Ser
NP_001229819.2:p.Ala78Ser
NC_000007.13:g.50607696C>A
NM_000790.3:c.232G>T
NR_033845.1:n.346C>A

Protein change:

A78S

Links:

dbSNP: rs140276979

NCBI 1000 Genomes Browser:

rs140276979

Molecular consequence:

NM_001242886.2:c.202-2019G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001242888.2:c.201+3887G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000790.4:c.232G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001082971.2:c.232G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242887.2:c.232G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242889.2:c.232G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001242890.2:c.232G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_033845.1:n.346C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Deficiency of aromatic-L-amino-acid decarboxylase
Synonyms:: DDC deficiency; Aromatic amino acid decarboxylase deficiency; Dopa decarboxylase deficiency
Identifiers:: MONDO: MONDO:0012084; MedGen: C1291564; Orphanet: 35708; OMIM: 608643

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ankyrin repeat domain-containing protein 49 [Mus musculus]
ankyrin repeat domain-containing protein 49 [Mus musculus]
gi|22165398|ref|NP_062657.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001393329	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 17, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001393329

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 17, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001393329.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 78 of the DDC protein (p.Ala78Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with DDC-related conditions. ClinVar contains an entry for this variant (Variation ID: 949757). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt DDC protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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