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NM_032808.7(LINGO1):c.1825G>A (p.Ala609Thr) AND Intellectual disability, autosomal recessive 64

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 1, 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:
RCV001839246.1

Allele description [Variation Report for NM_032808.7(LINGO1):c.1825G>A (p.Ala609Thr)]

NM_032808.7(LINGO1):c.1825G>A (p.Ala609Thr)

Gene:
LINGO1:leucine rich repeat and Ig domain containing 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q24.3
Genomic location:
Preferred name:
NM_032808.7(LINGO1):c.1825G>A (p.Ala609Thr)
HGVS:
  • NC_000015.10:g.77614082C>T
  • NM_001301186.2:c.1807G>A
  • NM_001301187.2:c.1807G>A
  • NM_001301189.2:c.1807G>A
  • NM_001301191.2:c.1807G>A
  • NM_001301192.2:c.1807G>A
  • NM_001301194.2:c.1807G>A
  • NM_001301195.2:c.1807G>A
  • NM_001301197.2:c.1807G>A
  • NM_001301198.2:c.1807G>A
  • NM_001301199.2:c.1807G>A
  • NM_001301200.2:c.1807G>A
  • NM_032808.5:c.1825G>A
  • NM_032808.7:c.1825G>AMANE SELECT
  • NP_001288115.1:p.Ala603Thr
  • NP_001288116.1:p.Ala603Thr
  • NP_001288118.1:p.Ala603Thr
  • NP_001288120.1:p.Ala603Thr
  • NP_001288121.1:p.Ala603Thr
  • NP_001288123.1:p.Ala603Thr
  • NP_001288124.1:p.Ala603Thr
  • NP_001288126.1:p.Ala603Thr
  • NP_001288127.1:p.Ala603Thr
  • NP_001288128.1:p.Ala603Thr
  • NP_001288129.1:p.Ala603Thr
  • NP_116197.4:p.Ala609Thr
  • NC_000015.9:g.77906424C>T
  • NM_001301191.1:c.1807G>A
Protein change:
A603T
Links:
dbSNP: rs367728067
NCBI 1000 Genomes Browser:
rs367728067
Molecular consequence:
  • NM_001301186.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301187.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301189.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301191.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301192.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301194.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301195.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301197.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301198.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301199.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001301200.2:c.1807G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032808.7:c.1825G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Intellectual disability, autosomal recessive 64
Synonyms:
Mental retardation, autosomal recessive 64; INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 64
Identifiers:
MONDO: MONDO:0020846; MedGen: C4748192; OMIM: 618103

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002099216New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Apr 1, 2021) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002099216.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The homozygous missense c.1807G>A (p.Ala603Thr) variant identified in exon 6 (of 6) of the LINGO1 gene has not been reported in affected individuals in the literature. The variant has 0.00001971 allele frequency in the gnomAD(v3) database (3 out of 152170 heterozygous alleles, no homozygotes) suggesting it is not a common benign variant in the populations represented in that database. The variant affects a moderately conserved residue. In silico tools show conflicting predictions about potential pathogenicity of this variant. Based on the available evidence, the homozygous missense c.1807G>A (p.Ala603Thr) variant identified in the LINGO1 gene is reported as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: May 7, 2024