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

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Apr 11, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000490429.2

Allele description

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)

Name:: Geroderma osteodysplastica (GO)
Synonyms:: WALT DISNEY DWARFISM
Identifiers:: MONDO: MONDO:0009271; MedGen: C0432255; Orphanet: 2078; OMIM: 231070

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267348	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 18, 2016)	germline	reference population	PubMed (2) [See all records that cite these PMIDs] 18997784, 25741868
SCV004048838	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 11, 2023)	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

SCV000267348

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 18, 2016)

germline

reference population

PubMed (2)
[See all records that cite these PMIDs]

SCV004048838

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 11, 2023)

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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
East Asian	germline	unknown	1	not provided	not provided	not provided	not provided	reference population

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267348.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East Asian	1	not provided	not provided	reference population	PubMed (2)

#	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		1	not provided	not provided	not provided

From Genome-Nilou Lab, SCV004048838.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jan 13, 2025

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