NM_007255.3(B4GALT7):c.38G>A (p.Trp13Ter) AND Ehlers-Danlos syndrome progeroid type

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 21, 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:: RCV000344285.5

Allele description [Variation Report for NM_007255.3(B4GALT7):c.38G>A (p.Trp13Ter)]

NM_007255.3(B4GALT7):c.38G>A (p.Trp13Ter)

Genes:

LOC129995400:ATAC-STARR-seq lymphoblastoid silent region 16704 [Gene]
B4GALT7:beta-1,4-galactosyltransferase 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q35.3

Genomic location:

Preferred name:

NM_007255.3(B4GALT7):c.38G>A (p.Trp13Ter)

Other names:

p.Trp13*

HGVS:

NC_000005.10:g.177600248G>A
NG_015977.1:g.5131G>A
NG_051237.1:g.13101G>A
NM_007255.3:c.38G>AMANE SELECT
NP_009186.1:p.Trp13Ter
NC_000005.9:g.177027249G>A
NM_007255.2:c.38G>A

Protein change:

W13*

Links:

dbSNP: rs200503833

NCBI 1000 Genomes Browser:

rs200503833

Molecular consequence:

NM_007255.3:c.38G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Ehlers-Danlos syndrome progeroid type
Synonyms:: Ehlers-Danlos syndrome, spondylodysplastic type
Identifiers:: MONDO: MONDO:0007526; MedGen: CN030853; Orphanet: 75496

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000766704	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 21, 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

SCV000766704

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 21, 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, SCV000766704.3

#	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 creates a premature translational stop signal (p.Trp13*) in the B4GALT7 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in B4GALT7 cause disease. This variant is present in population databases (rs200503833, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with B4GALT7-related conditions. ClinVar contains an entry for this variant (Variation ID: 282261). 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: Nov 18, 2024

ClinVar

Relating variation to medicine