NM_001177316.2(SLC34A3):c.304+2T>C AND Autosomal recessive hypophosphatemic bone disease

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Dec 19, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000513447.8

Allele description [Variation Report for NM_001177316.2(SLC34A3):c.304+2T>C]

NM_001177316.2(SLC34A3):c.304+2T>C

Gene:

SLC34A3:solute carrier family 34 member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_001177316.2(SLC34A3):c.304+2T>C

HGVS:

NC_000009.12:g.137232705T>C
NG_017008.2:g.6805T>C
NM_001177316.2:c.304+2T>CMANE SELECT
NM_001177317.2:c.304+2T>C
NM_080877.3:c.304+2T>C
NC_000009.11:g.140127157T>C
NM_080877.2:c.304+2T>C

Links:

dbSNP: rs201293634

NCBI 1000 Genomes Browser:

rs201293634

Molecular consequence:

NM_001177316.2:c.304+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001177317.2:c.304+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_080877.3:c.304+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Observations:

Condition(s)

Name:: Autosomal recessive hypophosphatemic bone disease (HHRH)
Synonyms:: HYPERCALCIURIC RICKETS; Hypophosphatemic rickets with hypercalciuria
Identifiers:: MONDO: MONDO:0009431; MedGen: C1853271; Orphanet: 157215; OMIM: 241530

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000608389	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	criteria provided, single submitter (Classification criteria August 2017)	Pathogenic (Sep 30, 2017)	paternal	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV001521095	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 19, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002786625	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 14, 2022)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000608389

Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München

criteria provided, single submitter

(Classification criteria August 2017)

Pathogenic
(Sep 30, 2017)

paternal

clinical testing

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

Citation Link,

SCV001521095

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 19, 2022)

unknown

clinical testing

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

SCV002786625

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 14, 2022)

unknown

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Hereditary hypophosphatemic rickets with hypercalciuria is caused by mutations in the sodium-phosphate cotransporter gene SLC34A3.

Lorenz-Depiereux B, Benet-Pages A, Eckstein G, Tenenbaum-Rakover Y, Wagenstaller J, Tiosano D, Gershoni-Baruch R, Albers N, Lichtner P, Schnabel D, Hochberg Z, Strom TM.

Am J Hum Genet. 2006 Feb;78(2):193-201. Epub 2005 Dec 9.

PubMed [citation]

PMID:: 16358215
PMCID:: PMC1380229

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 Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV000608389.1

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

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

From Baylor Genetics, SCV001521095.2

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

#	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

From Fulgent Genetics, Fulgent Genetics, SCV002786625.1

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

#	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: Sep 29, 2024

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