NM_000478.6(ALPL):c.211C>T (p.Arg71Cys) AND Infantile hypophosphatasia

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jan 15, 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:: RCV000014649.25

Allele description [Variation Report for NM_000478.6(ALPL):c.211C>T (p.Arg71Cys)]

NM_000478.6(ALPL):c.211C>T (p.Arg71Cys)

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.211C>T (p.Arg71Cys)

Other names:

R54C

HGVS:

NC_000001.11:g.21561126C>T
NG_008940.1:g.56762C>T
NM_000478.6:c.211C>TMANE SELECT
NM_001127501.4:c.46C>T
NM_001177520.3:c.66+381C>T
NM_001369803.2:c.211C>T
NM_001369804.2:c.211C>T
NM_001369805.2:c.211C>T
NP_000469.3:p.Arg71Cys
NP_001120973.2:p.Arg16Cys
NP_001356732.1:p.Arg71Cys
NP_001356733.1:p.Arg71Cys
NP_001356734.1:p.Arg71Cys
NC_000001.10:g.21887619C>T
NM_000478.4:c.211C>T
NM_000478.5:c.211C>T
P05186:p.Arg71Cys

Protein change:

R16C; ARG54CYS

Links:

UniProtKB: P05186#VAR_006149; OMIM: 171760.0002; dbSNP: rs121918001

NCBI 1000 Genomes Browser:

rs121918001

Molecular consequence:

NM_001177520.3:c.66+381C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000478.6:c.211C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127501.4:c.46C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369803.2:c.211C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369804.2:c.211C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001369805.2:c.211C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Infantile hypophosphatasia
Identifiers:: MedGen: C0268412; Orphanet: 436; OMIM: 241500

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000034904	OMIM	no assertion criteria provided	Pathogenic (Oct 15, 1992)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000797139	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Jan 15, 2018)	unknown	clinical testing	PubMed (6) [See all records that cite these PMIDs] 12162492, 20383509, 1409720, 19500388, 10839996, 28401263 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000034904

OMIM

no assertion criteria provided

Pathogenic
(Oct 15, 1992)

germline

literature only

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

SCV000797139

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(Jan 15, 2018)

unknown

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Kinetic characterization of hypophosphatasia mutations with physiological substrates.

Di Mauro S, Manes T, Hessle L, Kozlenkov A, Pizauro JM, Hoylaerts MF, Millán JL.

J Bone Miner Res. 2002 Aug;17(8):1383-91.

PubMed [citation]

PMID:: 12162492

Whole-body MRI in the childhood form of hypophosphatasia.

Beck C, Morbach H, Wirth C, Beer M, Girschick HJ.

Rheumatol Int. 2011 Oct;31(10):1315-20. doi: 10.1007/s00296-010-1493-3. Epub 2010 Apr 10.

PubMed [citation]

PMID:: 20383509

See all PubMed Citations (6)

Details of each submission

From OMIM, SCV000034904.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In fibroblasts from a 5-month-old boy with hypophosphatasia (241500) who died at 6 months of age, Henthorn et al. (1992) identified compound heterozygosity for 2 mutations in the ALPL gene: a 387C-T transition in exon 4, resulting in an arg54-to-cys (R54C) substitution, and a 1057A-C transversion in exon 9, resulting in an asp277-to-ala (D277A) substitution (171760.0003).

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

From Counsyl, SCV000797139.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

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

Last Updated: Oct 13, 2024

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