VCV000194279.27 - ClinVar

NM_001177316.2(SLC34A3):c.1454G>A (p.Arg485His)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(6)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Benign/Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001177316.2(SLC34A3):c.1454G>A (p.Arg485His)

Variation ID: 194279 Accession: VCV000194279.27

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9q34.3 9: 137236070 (GRCh38) [ NCBI UCSC ] 9: 140130522 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Jun 28, 2015	Oct 20, 2024	Jan 22, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001177316.2:c.1454G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001170787.2:p.Arg485His	missense
NM_001177317.2:c.1454G>A	NP_001170788.2:p.Arg485His	missense
NM_080877.3:c.1454G>A	NP_543153.2:p.Arg485His	missense
NC_000009.12:g.137236070G>A
NC_000009.11:g.140130522G>A
NG_017008.2:g.10170G>A

... more HGVS ... less HGVS

Protein change

R485H

Other names

Canonical SPDI

NC_000009.12:137236069:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00060 (A)

Allele frequency Help The frequency of the allele represented by this VCV record.

1000 Genomes Project 30x 0.00047

1000 Genomes Project 0.00060

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00139

The Genome Aggregation Database (gnomAD) 0.00215

The Genome Aggregation Database (gnomAD), exomes 0.00253

Exome Aggregation Consortium (ExAC) 0.00296

Links

ClinGen: CA201090 dbSNP: rs138872455 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
SLC34A3		-	-	GRCh38 GRCh37	606	723

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Benign (1)	criteria provided, single submitter	Apr 22, 2015	RCV000174613.4
not provided	Benign/Likely benign (2)	criteria provided, multiple submitters, no conflicts	Jan 22, 2024	RCV000889994.19
Autosomal recessive hypophosphatemic bone disease	Benign/Likely benign (2)	criteria provided, multiple submitters, no conflicts	Mar 17, 2022	RCV000988311.4
SLC34A3-related disorder	Likely benign (1)	no assertion criteria provided	May 13, 2020	RCV003955028.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Benign (Jan 22, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001033715.6 First in ClinVar: Dec 17, 2019 Last updated: Feb 14, 2024
Benign (Apr 22, 2015)	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000225935.5 First in ClinVar: Jun 28, 2015 Last updated: Jun 28, 2015	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SLC34A3 Number of individuals with the variant: 3 Sex: mixed
Benign (May 28, 2019)	criteria provided, single submitter (Mendelics Assertion Criteria 2017) Method: clinical testing	Autosomal recessive hypophosphatemic bone disease Affected status: unknown Allele origin: unknown	Mendelics Accession: SCV001137979.1 First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020
Likely benign (Mar 17, 2022)	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021) Method: clinical testing	Autosomal recessive hypophosphatemic bone disease Affected status: unknown Allele origin: germline	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories Accession: SCV003800362.2 First in ClinVar: Feb 13, 2023 Last updated: Mar 04, 2023
Likely benign (Sep 01, 2023)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV004164025.10 First in ClinVar: Nov 20, 2023 Last updated: Oct 20, 2024	Comment: SLC34A3: BS2 Number of individuals with the variant: 6
Likely benign (May 13, 2020)	no assertion criteria provided Method: clinical testing	SLC34A3-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004774138.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SLC34A3	-	-	-	-

Text-mined citations for rs138872455 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_001177316.2(SLC34A3):c.1454G>A (p.Arg485His)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs138872455 ...