NM_022787.4(NMNAT1):c.115+1G>A AND Leber congenital amaurosis 9

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

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 13, 2021
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:: RCV002003843.3

Allele description

NM_022787.4(NMNAT1):c.115+1G>A

Gene:

NMNAT1:nicotinamide nucleotide adenylyltransferase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.22

Genomic location:

Preferred name:

NM_022787.4(NMNAT1):c.115+1G>A

HGVS:

NC_000001.11:g.9972189G>A
NG_032954.1:g.33762G>A
NG_032954.2:g.34268G>A
NM_001297778.1:c.115+1G>A
NM_001297779.2:c.115+1G>A
NM_022787.4:c.115+1G>AMANE SELECT
NC_000001.10:g.10032247G>A

Links:

dbSNP: rs779434083

NCBI 1000 Genomes Browser:

rs779434083

Molecular consequence:

NM_001297778.1:c.115+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001297779.2:c.115+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_022787.4:c.115+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Leber congenital amaurosis 9 (LCA9)
Synonyms:: LCA 9; Amaurosis congenita of Leber, type 9; LCA9 Leber Congenital Amaurosis
Identifiers:: MONDO: MONDO:0012056; MedGen: C1837873; Orphanet: 65; OMIM: 608553

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002276778	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Oct 13, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16199547, 22842229, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002276778

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Oct 13, 2021)

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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Mutations in NMNAT1 cause Leber congenital amaurosis with early-onset severe macular and optic atrophy.

Perrault I, Hanein S, Zanlonghi X, Serre V, Nicouleau M, Defoort-Delhemmes S, Delphin N, Fares-Taie L, Gerber S, Xerri O, Edelson C, Goldenberg A, Duncombe A, Le Meur G, Hamel C, Silva E, Nitschke P, Calvas P, Munnich A, Roche O, Dollfus H, Kaplan J, et al.

Nat Genet. 2012 Sep;44(9):975-7. doi: 10.1038/ng.2357. Epub 2012 Jul 29.

PubMed [citation]

PMID:: 22842229

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002276778.3

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

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Disruption of this splice site has been observed in individual(s) with Leber congenital amaurosis (Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change affects a donor splice site in intron 2 of the NMNAT1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in NMNAT1 are known to be pathogenic (PMID: 22842229).

#	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 20, 2024

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