NM_014236.4(GNPAT):c.569-3T>G AND Rhizomelic chondrodysplasia punctata type 2

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

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Mar 17, 2024
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:: RCV001844353.8

Allele description

NM_014236.4(GNPAT):c.569-3T>G

Gene:

GNPAT:glyceronephosphate O-acyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q42.2

Genomic location:

Preferred name:

NM_014236.4(GNPAT):c.569-3T>G

HGVS:

NC_000001.11:g.231265290T>G
NG_008240.2:g.29118T>G
NM_001316350.2:c.386-3T>G
NM_014236.3:c.569-3T>G
NM_014236.4:c.569-3T>GMANE SELECT
NC_000001.10:g.231401036T>G
NM_014236.4:c.569-3T>G

Links:

dbSNP: rs745869264

NCBI 1000 Genomes Browser:

rs745869264

Molecular consequence:

NM_001316350.2:c.386-3T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_014236.4:c.569-3T>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Rhizomelic chondrodysplasia punctata type 2 (RCDP2)
Synonyms:: Dihydroxyacetonephosphate acyltransferase deficiency; Peroxisomal dihydroxyacetonephosphate acyltransferase deficiency; Chondrodysplasia punctata, rhizomelic, due to dihydroxyacetonephosphate acyltransferase deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009112; MedGen: C1857242; Orphanet: 177; OMIM: 222765

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001870475	Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre	no assertion criteria provided	Pathogenic (Apr 29, 2021)	germline	research
SCV003927850	Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)	no assertion criteria provided	Uncertain significance (Apr 1, 2023)	germline	clinical testing
SCV004804848	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 17, 2024)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001870475

Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre

no assertion criteria provided

Pathogenic
(Apr 29, 2021)

germline

research

SCV003927850

Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)

no assertion criteria provided

Uncertain significance
(Apr 1, 2023)

germline

clinical testing

SCV004804848

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 17, 2024)

germline

research

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, research
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	research

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 Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre, SCV001870475.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), SCV003927850.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004804848.2

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

#	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: Apr 6, 2024

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