1. Panels
  2. Nephrocalcinosis or nephrolithiasis
The latest signed off version for the GMS is v5.0. The current version, shown here, may differ from the signed-off version.

Nephrocalcinosis or nephrolithiasis (Version 5.5)

Level 2: Renal

Relevant disorders: Renal tract calcification (or Nephrolithiasis or nephrocalcinosis), Renal tract calcification (or Nephrolithiasis/nephrocalcinosis), R256
Panel types: Rare Disease 100K, GMS Rare Disease Virtual, GMS Rare Disease, Component Of Super Panel, GMS signed-off
Latest signed off version: v5.0 (30 Apr 2025)
Previously signed off versions: v4.16, v4.0, v3.0, v2.2
Previous code: 553f94d5bb5a1616e5ed45a5
Description
This panel is used for clinical indication 'R256 Nephrocalcinosis or nephrolithiasis' in the NHS Genomic Medicine Service.

Further information on the testing criteria and any overlapping clinical indications can be found within (https://www.england.nhs.uk/publication/national-genomic-test-directories/) under 'R256 Nephrocalcinosis or nephrolithiasis'.

A version of this panel has been signed off under NHS Genomic Medicine Service governance (see 'Latest signed off version' in the panel header information).

This panel will continue to be curated based on external reviews and Genomics England curation. New changes will be reflected in an increase to the minor version of the panel and details of these can be viewed in the 'Panel Activity' page. Periodically, these changes will be reviewed by a NHS Genomic Medicine Service evaluation process. The content that is agreed for the GMS panels will be reflected in an updated signed off version number.

CNVs, STRs and genes encoded by the mitochondrial genome may not be routinely included in the analysis where the panel is NOT delivered by WGS. Please contact your Genomic Laboratory Hub for information regarding specific queries.

This panel was originally developed for the 100,000 Genomes Project and is still being used for participants in the project. For the rare disease eligibility criteria refer to: https://www.genomicsengland.co.uk/rarediseasecriteria100K
Panel Activity

14 reviewers

  • Ellen McDonagh (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Fiona Karet (Universit y of Cambridge)

    Group: GeCIP domain
    Workplace: NHS clinical service

  • Shabbir Moochhala (UCL Centre for Nephrology)

    Group: GeCIP domain
    Workplace: NHS clinical service

  • Ellen Thomas (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Sarah Leigh (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Rebecca Foulger (Genomics England curator)

    Group: Other
    Workplace: Other

  • Louise Daugherty (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Eleanor Williams (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Zornitza Stark (Australian Genomics)

    Group: Other
    Workplace: Other clinical service

  • Detlef Bockenhauer (GOSH-UCL)

    Group: GeCIP domain
    Workplace: NHS clinical service

  • Arina Puzriakova (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Celia Duff-Farrier (North Bristol NHS Trust)

    Group: NHS Genomic Medicine Centre
    Workplace: NHS diagnostic lab

  • Achchuthan Shanmugasundram (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Ida Ertmanska (Genomics England Curator)

    Group: Other
    Workplace: Other

51 Entities

51 reviewed, 35 green

List Entity Reviews Mode of inheritance Details
51 Entitiess
Green List (high evidence)
AGXT
3 reviews
2 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Primary Hyperoxaluria Type 1
  • Primary Hyperoxaluria
  • Hyperoxaluria, primary, type 1, 259900
  • Hyperoxaluria
  • primary hyperoxaluria
Tags
Green List (high evidence)
APRT
1 review
 BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • Adenine phosphoribosyltransferase deficiency 614723
Tags
Green List (high evidence)
ATP6V0A4
5 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Expert
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Distal renal tubular acidosis 3, with or without sensorineural hearing loss, OMIM:602722
Tags
Green List (high evidence)
ATP6V1B1
4 reviews
2 green 		BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Expert
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Distal renal tubular acidosis 2 with progressive sensorineural hearing loss, OMIM:267300
  • renal tubular acidosis, distal, 2, with progressive sensorineural hearing loss, MONDO:0009968
Tags
Green List (high evidence)
BSND
3 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Bartter Syndrome
  • Bartter syndrome, type 4a, 602522
  • Sensorineural deafness with mild renal dysfunction, 602522
Tags
Green List (high evidence)
CA2
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • Osteopetrosis, autosomal recessive 3, with renal tubular acidosis
Tags
Green List (high evidence)
CASR
3 reviews
1 green 		BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Expert
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Familial Hypocalciuric Hypercalcemia
  • Hypocalciuric hypercalcemia, type I, 145980Hyperparathyroidism, neonatal, 239200Hypocalcemia, autosomal dominant, 601198Hypocalcemia, autosomal dominant, with Bartter syndrome, 601198{Epilepsy idiopathic generalized, susceptibility to,
  • Hypocalcemia (dominant)
  • Familial Hypocalciuric Hypercalcemia (dominant)
  • hypocalciuric hypercalcaemia
Tags
Green List (high evidence)
CLCN5
3 reviews
1 green 		X-LINKED: hemizygous mutation in males, biallelic mutations in females
Sources
  • Expert
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Dent Disease
  • Dent disease, 300009
  • Nephrolithiasis, type I, 310468Hypophosphatemic rickets, 300554
  • Proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis, 308990
  • Nephrocalcinosis with low molecular weight proteinuria and pregressive CKD
Tags
Green List (high evidence)
CLCNKB
5 reviews
2 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
  • NHS GMS
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Bartter syndrome, type 3, OMIM:607364
  • Bartter disease type 3, MONDO:0011822
  • Bartter syndrome, type 4b, digenic, OMIM:613090
  • Bartter disease type 4B, MONDO:0000909
Tags
  • monogenic-polygenic
Green List (high evidence)
CLDN16
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • Hypomagnesemia 3, renal, OMIM:248250
Tags
Green List (high evidence)
CLDN19
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • hypomagensemia with nephrocalcinosis
  • Hypomagnesemia 5, renal, with ocular involvement
Tags
Green List (high evidence)
CYP24A1
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Infantile Hypercalcemia
  • Hypercalcemia, infantile, 143880
  • Infantile hypercalcaemia
Tags
Green List (high evidence)
FAM20A
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • Amelogenesis imperfecta, type IG (enamel-renal syndrome) 204690
Tags
Green List (high evidence)
GRHPR
3 reviews
2 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Primary Hyperoxaluria
  • Primary Hyperoxaluria Type 2
  • Hyperoxaluria, primary, type II, 260000
  • Hyperoxaluria
Tags
Green List (high evidence)
HNF4A
4 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • Fanconi renotubular syndrome 4, with maturity-onset diabetes of the young, OMIM:616026
Tags
Green List (high evidence)
HOGA1
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Expert
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Primary Hyperoxaluria
  • Hyperoxaluria, primary, type III, 613616
  • Hyperoxaluria
Tags
Green List (high evidence)
HPRT1
3 reviews
1 green 		X-LINKED: hemizygous mutation in males, biallelic mutations in females
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • Hyperuricemia, HRPT-related, OMIM:300323
  • Lesch-Nyhan syndrome, OMIM:300322
Tags
Green List (high evidence)
KCNJ1
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Antenatal Bartter Syndrome
  • Bartter syndrome, type 2, 241200
  • Type 2 Bartter syndrome
  • often initial transient hyperkalemia
Tags
Green List (high evidence)
MOCOS
2 reviews
2 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Xanthinuria, type II, OMIM:603592
Tags
Green List (high evidence)
OCRL
4 reviews
1 green 		X-LINKED: hemizygous mutation in males, biallelic mutations in females
Sources
  • Expert
  • Expert Review Green
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Lowe syndrome, OMIM:309000
  • Dent disease 2, OMIM:300555
  • As for CLCN5 (Nephrocalcinosis with low molecular weight proteinuria and pregressive CKD) but may include intellectual disability and other features of Lowe syndrome
Tags
Green List (high evidence)
PHEX
2 reviews
1 green 		X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Sources
  • Expert list
  • Expert Review Green
  • Literature
Phenotypes
  • Hypophosphatemic rickets, X-linked dominant 307800
Tags
Green List (high evidence)
RRAGD
3 reviews
2 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • hypomagnesaemia
  • nephrocalcinosis
  • salt wasting
  • cardiomyopathy
  • tubular renal disease-cardiomyopathy syndrome, MONDO:0019130
Tags
Green List (high evidence)
SLC12A1
3 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Bartter syndrome, type 1, OMIM:601678
  • Bartter disease type 1, MONDO:0100344
Tags
  • monogenic-polygenic
Green List (high evidence)
SLC22A12
2 reviews
1 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • Hypouricemia, renal, 220150
Tags
Green List (high evidence)
SLC2A9
3 reviews
1 green 		BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • Hypouricemia, renal, 2, 612076
Tags
Green List (high evidence)
SLC34A1
2 reviews
1 green 		BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Nephrolithiasis/osteoporosis, hypophosphatemic, 1, 612286
  • Hypophosphatemic Nephrolithiasis/Osteoporosis
  • Hypophosphatemic Nephrolithiasis/Osteoporosis (recessive)
  • Nephrolithiasis with osteoporosis and hypophosphatemia
  • Nephrolithiasis with osteoporosis and hypophosphatemia
Tags
Green List (high evidence)
SLC34A3
5 reviews
2 green 		BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
  • NHS GMS
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Hypophosphatemic rickets with hypercalciuria, OMIM:241530
  • HHRH
  • hereditary hypophosphatemic rickets with hypercalciuria, MONDO:0009431
Tags
Green List (high evidence)
SLC3A1
2 reviews
1 green 		BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Expert
  • Expert Review Green
Phenotypes
  • Cystinuria 220100
Tags
Green List (high evidence)
SLC4A1
2 reviews
 BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Expert
  • Expert Review Green
Phenotypes
  • distal renal tubular acidosis
  • Renal tubular acidosis, distal, AD, 179800
  • Renal tubular acidosis, distal, AR 611590
Tags
Green List (high evidence)
SLC7A9
2 reviews
1 green 		BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Expert
  • Expert Review Green
Phenotypes
  • Cystinuria 220100
Tags
Green List (high evidence)
STRADA
3 reviews
1 green 1 red 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
Phenotypes
  • Polyhydramnios, megalencephaly, and symptomatic epilepsy, 611087
Tags
Green List (high evidence)
VIPAS39
3 reviews
 BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Arthrogryposis, renal dysfunction, and cholestasis 2, OMIM:613404
Tags
Green List (high evidence)
VPS33B
3 reviews
 BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Arthrogryposis, renal dysfunction, and cholestasis 1, OMIM:208085
Tags
Green List (high evidence)
WDR72
3 reviews
2 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Green
  • NHS GMS
Phenotypes
  • distal renal tubular acidosis, MONDO:0015827
  • Amelogenesis imperfecta, type IIA3, OMIM:613211
  • amelogenesis imperfecta hypomaturation type 2A3, MONDO:0013181
Tags
Green List (high evidence)
XDH
3 reviews
 BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Green
Phenotypes
  • Xanthinuria, type I, 278300
Tags
Amber List (moderate evidence)
SLC9A3R1
4 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert
  • Expert Review Amber
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Nephrolithiasis/osteoporosis, hypophosphatemic, 2, 612287
Tags
  • new-gene-name
Red List (low evidence)
ADCY10
4 reviews
1 green 1 red 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert
  • Expert Review Red
Tags
Red List (low evidence)
AGK
2 reviews
2 red 		Not set
Sources
  • Expert Review Red
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Hyperoxaluria, primary, type 1, 259900
Tags
Red List (low evidence)
AP2S1
2 reviews
2 red 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Red
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Hypocalciuric hypercalcemia, familial, type III, 600740
  • Familial hypocalciuric hypercalcemia type III
Tags
Red List (low evidence)
CLCNKA
4 reviews
1 red 		Other
Sources
  • Expert Review Red
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Bartter syndrome, type 4b, digenic, OMIM:613090
  • Bartter disease type 4B, MONDO:0000909
Tags
  • polygenic
Red List (low evidence)
FGF23
2 reviews
1 green 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert list
Tags
  • watchlist
Red List (low evidence)
GNA11
1 review
1 red 		Not set
Sources
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Hypocalciuric hypercalcemia, type II, 145981
Tags
Red List (low evidence)
SLC26A1
4 reviews
1 green 2 red 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Red
Phenotypes
  • Nephrolithiasis, calcium oxalate, MIM#167030
Tags
Red List (low evidence)
SLC26A6
1 review
 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Literature
Phenotypes
  • Enteric hyperoxaluria and nephrolithiasis
Tags
  • watchlist
Red List (low evidence)
SLC36A2
2 reviews
2 red 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
Tags
Red List (low evidence)
SLC6A19
3 reviews
2 red 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert
Tags
Red List (low evidence)
SLC6A20
2 reviews
2 red 		BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert
Tags
Red List (low evidence)
SLC9A3
2 reviews
2 red 		BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert
Tags
Red List (low evidence)
TRPM6
3 reviews
1 red 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Hypomagnesemia with Secondary Hypocalcemia
Tags
Red List (low evidence)
VDR
1 review
1 red 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert
Tags
Red List (low evidence)
ZNF365
4 reviews
1 green 1 red 		BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert
  • Expert Review Red
Phenotypes
  • Possible cause of uric acid stones
  • {Nephrolithiasis, uric acid, susceptibility to}
Tags

Major version comments

  • 2025-04-30 16:38 Eleanor Williams (Genomics England Curator) promoted panel to 5.0
    The content of this panel has been updated in accordance with changes agreed with the NHS Genomic Medicine Service. The panel was promoted to the next major version (5.0) following this.

    2023-03-22 15:47 Achchuthan Shanmugasundram (Genomics England Curator) promoted panel to 4.0
    The content of this panel has been updated in accordance with changes agreed with the NHS Genomic Medicine Service. The panel was promoted to the next major version (4.0) following this.

    2022-11-30 15:15 Achchuthan Shanmugasundram (Genomics England Curator) promoted panel to 3.0
    The content of this panel has been updated in accordance with changes agreed with the NHS Genomic Medicine Service. The panel was promoted to the next major version (3.0) following this.

    2019-12-04 14:45 Eleanor Williams (Genomics England Curator) promoted panel to 2.0
    The content of this panel (version 1.51) was signed off under NHS Genomic Medicine Service governance on 04/12/2019. The panel was promoted to the next major version (version 2.0) as a result of this.

    23.05.2016 - External reviews were evaluated, and with further curation of databases and literature, the gene panel was revised.

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