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NM_182548.4(LHFPL5):c.43C>T (p.His15Tyr) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 8, 2018
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:
RCV000218391.6

Allele description [Variation Report for NM_182548.4(LHFPL5):c.43C>T (p.His15Tyr)]

NM_182548.4(LHFPL5):c.43C>T (p.His15Tyr)

Gene:
LHFPL5:LHFPL tetraspan subfamily member 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.31
Genomic location:
Preferred name:
NM_182548.4(LHFPL5):c.43C>T (p.His15Tyr)
HGVS:
  • NC_000006.12:g.35805713C>T
  • NG_012184.2:g.5420C>T
  • NM_182548.4:c.43C>TMANE SELECT
  • NP_872354.1:p.His15Tyr
  • LRG_1352t1:c.43C>T
  • LRG_1352p1:p.His15Tyr
  • NC_000006.11:g.35773490C>T
  • NG_012184.1:g.5420C>T
  • NM_182548.3:c.43C>T
Protein change:
H15Y
Links:
dbSNP: rs149941106
NCBI 1000 Genomes Browser:
rs149941106
Molecular consequence:
  • NM_182548.4:c.43C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
5

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000271919Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Uncertain significance
(May 8, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided55not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000271919.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testing PubMed (1)

Description

Variant classified as Uncertain Significance - Favor Benign. The p.His15Tyr vari ant in LHFPL5 has been previously reported in 4 individuals with hearing loss by our laboratory; however, none of them had a variant affecting the other copy of the gene and one of these individuals had an alternate etiology of the hearing loss. This variant has been identified in 0.2% (67/34420 and 44/24030) of Latino and African chromosomes by the Genome Aggregation Database (gnomAD, http://gnom ad.broadinstitute.org; dbSNP rs149941106). Although this variant has been seen i n the general population, its frequency is not high enough to rule out a pathoge nic role. Computational prediction tools and conservation analysis do not provid e strong support for or against an impact to the protein. In summary, while the clinical significance of the p.His15Tyr variant is uncertain, the frequency data in the general population suggest that it is more likely to be benign. ACMG/AMP Criteria applied: BS1_Supporting.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided5not provided5not provided

Last Updated: Sep 29, 2024