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NM_000478.6(ALPL):c.127C>T (p.Leu43Phe) AND Adult hypophosphatasia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 9, 2019
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:
RCV001542259.1

Allele description [Variation Report for NM_000478.6(ALPL):c.127C>T (p.Leu43Phe)]

NM_000478.6(ALPL):c.127C>T (p.Leu43Phe)

Gene:
ALPL:alkaline phosphatase, biomineralization associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.12
Genomic location:
Preferred name:
NM_000478.6(ALPL):c.127C>T (p.Leu43Phe)
Other names:
dnSNP:rs148357203
HGVS:
  • NC_000001.11:g.21560691C>T
  • NG_008940.1:g.56327C>T
  • NM_000478.6:c.127C>TMANE SELECT
  • NM_001127501.4:c.-39C>T
  • NM_001177520.3:c.12C>T
  • NM_001369803.2:c.127C>T
  • NM_001369804.2:c.127C>T
  • NM_001369805.2:c.127C>T
  • NP_000469.3:p.Leu43Phe
  • NP_001170991.1:p.Ser4=
  • NP_001356732.1:p.Leu43Phe
  • NP_001356733.1:p.Leu43Phe
  • NP_001356734.1:p.Leu43Phe
  • NC_000001.10:g.21887184C>T
Protein change:
L43F
Links:
dbSNP: rs148357203
NCBI 1000 Genomes Browser:
rs148357203
Molecular consequence:
  • NM_001127501.4:c.-39C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000478.6:c.127C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369803.2:c.127C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369804.2:c.127C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001369805.2:c.127C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177520.3:c.12C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Adult hypophosphatasia
Identifiers:
MedGen: C0268413; Orphanet: 436; OMIM: 146300

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001760926NxGen MDx
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Dec 9, 2019) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot 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 NxGen MDx, SCV001760926.1

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

Description

This missense variant (c.127C>T) is in a hot-spot locus in on exon 3 of ALPL (PM1) resulting in a residue change from leucine to phenylalanine (p.Leu43Phe) which are both non-polar but differ in size. This variant has low allele frequency in gnomAD exomes (PM2) and has several pathogenic computational predictions (PP3). We interpret c.127C>T to be of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024