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NM_000899.5(KITLG):c.2T>A (p.Met1Lys) AND Autosomal dominant nonsyndromic hearing loss 69

Germline classification:
Uncertain significance (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:
RCV002283908.1

Allele description [Variation Report for NM_000899.5(KITLG):c.2T>A (p.Met1Lys)]

NM_000899.5(KITLG):c.2T>A (p.Met1Lys)

Gene:
KITLG:KIT ligand [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q21.32
Genomic location:
Preferred name:
NM_000899.5(KITLG):c.2T>A (p.Met1Lys)
HGVS:
  • NC_000012.12:g.88580277A>T
  • NG_012098.2:g.5185T>A
  • NM_000899.5:c.2T>AMANE SELECT
  • NM_003994.6:c.2T>A
  • NP_000890.1:p.Met1Lys
  • NP_003985.2:p.Met1Lys
  • LRG_1379t1:c.2T>A
  • LRG_1379:g.5185T>A
  • LRG_1379p1:p.Met1Lys
  • NC_000012.11:g.88974054A>T
Protein change:
M1K
Molecular consequence:
  • NM_000899.5:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_003994.6:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_000899.5:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003994.6:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Autosomal dominant nonsyndromic hearing loss 69
Synonyms:
Deafness, autosomal dominant 69; Deafness, autosomal dominant 69, unilateral or asymmetric
Identifiers:
MONDO: MONDO:0014738; MedGen: C4225241; Orphanet: 90635; OMIM: 616697

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0025730983billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 1, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical 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 3billion, SCV002573098.2

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

Description

The variant is not observed in the gnomAD v2.1.1 dataset. Start-lost is reinitiation of translation may occur at a downstream alternate start codon but still result in a loss or disruption of normal protein function as there have been pathogenic variants reported upstream of the alternate start codon. Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Sep 3, 2023