NM_012233.3(RAB3GAP1):c.1247del (p.Pro416fs) AND Warburg micro syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 10, 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:: RCV003397204.1

Allele description [Variation Report for NM_012233.3(RAB3GAP1):c.1247del (p.Pro416fs)]

NM_012233.3(RAB3GAP1):c.1247del (p.Pro416fs)

Gene:

RAB3GAP1:RAB3 GTPase activating protein catalytic subunit 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q21.3

Genomic location:

Preferred name:

NM_012233.3(RAB3GAP1):c.1247del (p.Pro416fs)

HGVS:

NC_000002.12:g.135132905del
NG_016972.1:g.85641del
NG_016972.2:g.85615del
NM_001172435.2:c.1247del
NM_012233.3:c.1247delMANE SELECT
NP_001165906.1:p.Pro416fs
NP_036365.1:p.Pro416fs
NC_000002.11:g.135890475del
NM_012233.2:c.1247del

Protein change:

P416fs

Links:

dbSNP: rs2468218576

NCBI 1000 Genomes Browser:

rs2468218576

Molecular consequence:

NM_001172435.2:c.1247del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012233.3:c.1247del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Warburg micro syndrome 1 (WARBM1)
Identifiers:: MONDO: MONDO:0010822; MedGen: C1838625; Orphanet: 2510; OMIM: 600118

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004102733	Daryl Scott Lab, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 10, 2023)	maternal	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

SCV004102733

Daryl Scott Lab, Baylor College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 10, 2023)

maternal

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	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Daryl Scott Lab, Baylor College of Medicine, SCV004102733.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	maternal	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: May 16, 2025

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