NM_152281.3(GORAB):c.408_409del (p.Lys137fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 7, 2023
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:: RCV001853387.3

Allele description [Variation Report for NM_152281.3(GORAB):c.408_409del (p.Lys137fs)]

NM_152281.3(GORAB):c.408_409del (p.Lys137fs)

Gene:

GORAB:golgin, RAB6 interacting [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q24.2

Genomic location:

Preferred name:

NM_152281.3(GORAB):c.408_409del (p.Lys137fs)

HGVS:

NC_000001.11:g.170539556_170539557del
NG_012237.1:g.12435_12436del
NM_001146039.2:c.408_409del
NM_001320252.2:c.-58_-57del
NM_152281.3:c.408_409delMANE SELECT
NP_001139511.2:p.Lys137fs
NP_689494.3:p.Lys137fs
NC_000001.10:g.170508696_170508697del
NC_000001.10:g.170508697_170508698del
NM_001146039.1:c.483_484delGA
NR_027397.2:n.466_467del

Protein change:

K137fs

Links:

dbSNP: rs1085307068

NCBI 1000 Genomes Browser:

rs1085307068

Molecular consequence:

NM_001320252.2:c.-58_-57del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001146039.2:c.408_409del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_152281.3:c.408_409del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_027397.2:n.466_467del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002178682	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 7, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18997784, 19681135, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002178682

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 7, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Gerodermia osteodysplastica is caused by mutations in SCYL1BP1, a Rab-6 interacting golgin.

Hennies HC, Kornak U, Zhang H, Egerer J, Zhang X, Seifert W, Kühnisch J, Budde B, Nätebus M, Brancati F, Wilcox WR, Müller D, Kaplan PB, Rajab A, Zampino G, Fodale V, Dallapiccola B, Newman W, Metcalfe K, Clayton-Smith J, Tassabehji M, Steinmann B, et al.

Nat Genet. 2008 Dec;40(12):1410-2. doi: 10.1038/ng.252. Epub 2008 Nov 9.

PubMed [citation]

PMID:: 18997784
PMCID:: PMC3122266

A novel missense mutation in SCYL1BP1 produces geroderma osteodysplastica phenotype indistinguishable from that caused by nullimorphic mutations.

Al-Dosari M, Alkuraya FS.

Am J Med Genet A. 2009 Oct;149A(10):2093-8. doi: 10.1002/ajmg.a.32996.

PubMed [citation]

PMID:: 19681135

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002178682.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 225381). This variant has not been reported in the literature in individuals affected with GORAB-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys162Serfs*24) in the GORAB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GORAB are known to be pathogenic (PMID: 18997784, 19681135).

#	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: Feb 28, 2024

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