NM_001126121.2(SLC25A19):c.775-1G>C AND Amish lethal microcephaly

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 12, 2018
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:: RCV000853269.1

Allele description [Variation Report for NM_001126121.2(SLC25A19):c.775-1G>C]

NM_001126121.2(SLC25A19):c.775-1G>C

Genes:

MIF4GD-DT:MIF4GD divergent transcript [Gene - HGNC]
SLC25A19:solute carrier family 25 member 19 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.1

Genomic location:

Preferred name:

NM_001126121.2(SLC25A19):c.775-1G>C

HGVS:

NC_000017.11:g.75273640C>G
NG_008274.1:g.20810G>C
NM_001126121.2:c.775-1G>CMANE SELECT
NM_001126122.2:c.775-1G>C
NM_021734.5:c.775-1G>C
NC_000017.10:g.73269721C>G
NM_001126121.1:c.775-1G>C
NR_036520.1:n.2342C>G

Links:

dbSNP: rs372041843

NCBI 1000 Genomes Browser:

rs372041843

Molecular consequence:

NR_036520.1:n.2342C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001126121.2:c.775-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001126122.2:c.775-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_021734.5:c.775-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Name:: Amish lethal microcephaly (MCPHA)
Synonyms:: Microcephaly, Amish type; THIAMINE METABOLISM DYSFUNCTION SYNDROME 3 (MICROCEPHALY TYPE)
Identifiers:: MONDO: MONDO:0011790; MedGen: C1846648; Orphanet: 99742; OMIM: 607196

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000996101	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 12, 2018)	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

SCV000996101

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 12, 2018)

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	yes	1	not provided	not provided	1	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 Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV000996101.1

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

Description

This canonical splice site variant is predicted to result in aberrant splicing of the SLC25A19 gene. This variant has not been previously reported in the literature, but SLC25A19 is predicted to be loss of function intolerant. There is one report of the variant in the public database of genetic variation, gnomAD, thus the variant is rare. Based on the predicted functional consequence of this variant and supporting evidence, the variant is classified as pathogenic.

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

Last Updated: Jun 10, 2023

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