NM_152222.2(RELT):c.260A>T (p.Asp87Val) AND Amelogenesis imperfecta

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 20, 2023
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:: RCV003482918.1

Allele description [Variation Report for NM_152222.2(RELT):c.260A>T (p.Asp87Val)]

NM_152222.2(RELT):c.260A>T (p.Asp87Val)

Gene:

RELT:RELT TNF receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.4

Genomic location:

Preferred name:

NM_152222.2(RELT):c.260A>T (p.Asp87Val)

HGVS:

NC_000011.10:g.73390894A>T
NM_032871.4:c.260A>T
NM_152222.2:c.260A>TMANE SELECT
NP_116260.2:p.Asp87Val
NP_689408.1:p.Asp87Val
NC_000011.9:g.73101939A>T

Protein change:

D87V

Molecular consequence:

NM_032871.4:c.260A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_152222.2:c.260A>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Amelogenesis imperfecta (AI)
Synonyms:: Congenital enamel hypoplasia
Identifiers:: MONDO: MONDO:0019507; MedGen: C0002452; OMIM: PS104500; Human Phenotype Ontology: HP:0000705

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004014054	Department Of Pediatric Dentistry, Peking University School And Hospital Of Stomatology	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 20, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 30506946, 32052416, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004014054

Department Of Pediatric Dentistry, Peking University School And Hospital Of Stomatology

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(May 20, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in RELT cause autosomal recessive amelogenesis imperfecta.

Kim JW, Zhang H, Seymen F, Koruyucu M, Hu Y, Kang J, Kim YJ, Ikeda A, Kasimoglu Y, Bayram M, Zhang C, Kawasaki K, Bartlett JD, Saunders TL, Simmer JP, Hu JC.

Clin Genet. 2019 Mar;95(3):375-383. doi: 10.1111/cge.13487. Epub 2018 Dec 21.

PubMed [citation]

PMID:: 30506946
PMCID:: PMC6392136

New missense variants in RELT causing hypomineralised amelogenesis imperfecta.

Nikolopoulos G, Smith CEL, Brookes SJ, El-Asrag ME, Brown CJ, Patel A, Murillo G, O'Connell MJ, Inglehearn CF, Mighell AJ.

Clin Genet. 2020 May;97(5):688-695. doi: 10.1111/cge.13721. Epub 2020 Feb 21.

PubMed [citation]

PMID:: 32052416
PMCID:: PMC7216828

See all PubMed Citations (3)

Details of each submission

From Department Of Pediatric Dentistry, Peking University School And Hospital Of Stomatology, SCV004014054.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	PubMed (3)

Description

Homozygous mutations in RELT have been reported to cause autosomal recessive AI. Multiple missense mutations have been reported to be associated with AI. The variant cosegregation with the disease in this family. The RELT variant (c.260A>T) is documented in the dbSNP database (rs771045558) with a minor allele frequency (MAF) count of 1/120740. This missense variant was predicted to be damaging, diseasing causing in SIFT (0.0, Deleterious), Polyphen2_HDIV (1.0, Probably damaging), MutationTaster (1, Disease-causing) and CADD (score: 24.6). These nucleotide change in RELT were absent in 144 ethnically matched normal controls. Amino-acid alignment analysis revealed that the affected residues were highly conserved among different species.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Feb 14, 2024

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