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NM_001199799.2(ILDR1):c.206C>A (p.Pro69His) AND Autosomal recessive nonsyndromic hearing loss 42

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 1, 2022
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:
RCV002283615.1

Allele description [Variation Report for NM_001199799.2(ILDR1):c.206C>A (p.Pro69His)]

NM_001199799.2(ILDR1):c.206C>A (p.Pro69His)

Gene:
ILDR1:immunoglobulin like domain containing receptor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q13.33
Genomic location:
Preferred name:
NM_001199799.2(ILDR1):c.206C>A (p.Pro69His)
HGVS:
  • NC_000003.12:g.122007014G>T
  • NG_031870.2:g.58541C>A
  • NM_001199799.2:c.206C>AMANE SELECT
  • NM_001199800.2:c.206C>A
  • NM_175924.4:c.206C>A
  • NP_001186728.1:p.Pro69His
  • NP_001186729.1:p.Pro69His
  • NP_787120.1:p.Pro69His
  • LRG_1377t1:c.206C>A
  • LRG_1377:g.58541C>A
  • LRG_1377p1:p.Pro69His
  • NC_000003.11:g.121725861G>T
Protein change:
P69H
Molecular consequence:
  • NM_001199799.2:c.206C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199800.2:c.206C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_175924.4:c.206C>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Autosomal recessive nonsyndromic hearing loss 42
Synonyms:
Deafness, autosomal recessive 42
Identifiers:
MONDO: MONDO:0012326; MedGen: C1864818; Orphanet: 90636; OMIM: 609646

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0025725443billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Sep 1, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Citations

PubMed

Downsloping high-frequency hearing loss due to inner ear tricellular tight junction disruption by a novel ILDR1 mutation in the Ig-like domain.

Kim NK, Higashi T, Lee KY, Kim AR, Kitajiri S, Kim MY, Chang MY, Kim V, Oh SH, Kim D, Furuse M, Park WY, Choi BY.

PLoS One. 2015;10(2):e0116931. doi: 10.1371/journal.pone.0116931.

PubMed [citation]
PMID:
25668204
PMCID:
PMC4323246

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 3billion, SCV002572544.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.003%). While this variant results in missense change, protein truncation variants are a common disease-causing mechanism. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 25668204). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.79; 3Cnet: 0.38). Same nucleotide change resulting in same amino acid change has been previously reported to be associated with ILDR1-related disorder (PMID: 25668204). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Sep 24, 2022