NM_014336.5(AIPL1):c.401A>T (p.Tyr134Phe) AND Leber congenital amaurosis 4

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Dec 4, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV001082876.3

Allele description [Variation Report for NM_014336.5(AIPL1):c.401A>T (p.Tyr134Phe)]

NM_014336.5(AIPL1):c.401A>T (p.Tyr134Phe)

Gene:
AIPL1:aryl hydrocarbon receptor interacting protein like 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p13.2
Genomic location:
Preferred name:
NM_014336.5(AIPL1):c.401A>T (p.Tyr134Phe)
HGVS:
  • NC_000017.11:g.6428382T>A
  • NG_008474.1:g.11818A>T
  • NM_001033054.3:c.277-1325A>T
  • NM_001033055.3:c.221A>T
  • NM_001285399.3:c.365A>T
  • NM_001285400.3:c.335A>T
  • NM_001285401.3:c.401A>T
  • NM_001285402.2:c.284A>T
  • NM_001285403.3:c.401A>T
  • NM_014336.5:c.401A>TMANE SELECT
  • NP_001028227.1:p.Tyr74Phe
  • NP_001272328.1:p.Tyr122Phe
  • NP_001272329.1:p.Tyr112Phe
  • NP_001272330.1:p.Tyr134Phe
  • NP_001272331.1:p.Tyr95Phe
  • NP_001272332.1:p.Tyr134Phe
  • NP_055151.3:p.Tyr134Phe
  • NC_000017.10:g.6331702T>A
  • NM_014336.3:c.401A>T
  • NM_014336.4:c.401A>T
  • Q9NZN9:p.Tyr134Phe
Protein change:
Y112F
Links:
UniProtKB: Q9NZN9#VAR_050627; dbSNP: rs16955851
NCBI 1000 Genomes Browser:
rs16955851
Molecular consequence:
  • NM_001033054.3:c.277-1325A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001033055.3:c.221A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001285399.3:c.365A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001285400.3:c.335A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001285401.3:c.401A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001285402.2:c.284A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001285403.3:c.401A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_014336.5:c.401A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Leber congenital amaurosis 4 (LCA4)
Synonyms:
Amaurosis congenita of Leber, type 4
Identifiers:
MONDO: MONDO:0011458; MedGen: C1858386; OMIM: 604393

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000764117Invitaecriteria provided, single submitter
Benign
(Dec 4, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001284472Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Apr 27, 2017)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

An assessment of the apex microarray technology in genotyping patients with Leber congenital amaurosis and early-onset severe retinal dystrophy.

Henderson RH, Waseem N, Searle R, van der Spuy J, Russell-Eggitt I, Bhattacharya SS, Thompson DA, Holder GE, Cheetham ME, Webster AR, Moore AT.

Invest Ophthalmol Vis Sci. 2007 Dec;48(12):5684-9.

PubMed [citation]
PMID:
18055820
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000764117.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV001284472.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 10, 2021

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