NM_015681.6(B9D1):c.55A>C (p.Ser19Arg) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 23, 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:: RCV003010400.3

Allele description [Variation Report for NM_015681.6(B9D1):c.55A>C (p.Ser19Arg)]

NM_015681.6(B9D1):c.55A>C (p.Ser19Arg)

Genes:

LOC130060455:ATAC-STARR-seq lymphoblastoid silent region 8288 [Gene]
B9D1:B9 domain containing 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p11.2

Genomic location:

Preferred name:

NM_015681.6(B9D1):c.55A>C (p.Ser19Arg)

HGVS:

NC_000017.11:g.19362515T>G
NG_031885.2:g.20679A>C
NM_001321214.2:c.55A>C
NM_001321215.3:c.55A>C
NM_001321216.2:c.55A>C
NM_001321217.2:c.55A>C
NM_001321218.2:c.55A>C
NM_001321219.2:c.55A>C
NM_001330149.2:c.55A>C
NM_001368769.2:c.-297-2127A>C
NM_015681.6:c.55A>CMANE SELECT
NP_001308143.1:p.Ser19Arg
NP_001308144.1:p.Ser19Arg
NP_001308145.1:p.Ser19Arg
NP_001308146.1:p.Ser19Arg
NP_001308147.1:p.Ser19Arg
NP_001308148.1:p.Ser19Arg
NP_001317078.1:p.Ser19Arg
NP_056496.1:p.Ser19Arg
LRG_686t1:c.55A>C
LRG_686:g.20679A>C
LRG_686p1:p.Ser19Arg
NC_000017.10:g.19265828T>G

Protein change:

S19R

Molecular consequence:

NM_001368769.2:c.-297-2127A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001321214.2:c.55A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321215.3:c.55A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321216.2:c.55A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321217.2:c.55A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321218.2:c.55A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321219.2:c.55A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001330149.2:c.55A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_015681.6:c.55A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial aplasia of the vermis
Synonyms:: CEREBELLOPARENCHYMAL DISORDER IV; Joubert syndrome; Cerebelloparenchymal disorder 4; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018772; MedGen: C0431399; Orphanet: 475; OMIM: PS213300

Name:: Meckel-Gruber syndrome
Synonyms:: DYSENCEPHALIA SPLANCHNOCYSTICA; Gruber syndrome; Dysencephalia splachnocystica
Identifiers:: MONDO: MONDO:0018921; MedGen: C0265215; OMIM: PS249000

Recent activity

Clear Turn Off Turn On

Scopus umbretta voucher UMMZ-T078 glyceraldehyde-3-phosphate dehydrogenase (GAPD...
Scopus umbretta voucher UMMZ-T078 glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, partial cds
gi|1146075808|gb|KX534661.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003308786	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 23, 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

SCV003308786

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 23, 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, SCV003308786.2

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

Description

This variant has not been reported in the literature in individuals affected with B9D1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 19 of the B9D1 protein (p.Ser19Arg). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C15"). 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

ClinVar

Relating variation to medicine