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Fetal anomalies

Gene: FLVCR1

Green List (high evidence)
FLVCR1 (feline leukemia virus subgroup C cellular receptor 1)
EnsemblGeneIds (GRCh38): ENSG00000162769
EnsemblGeneIds (GRCh37): ENSG00000162769
OMIM: 609144, Gene2Phenotype
FLVCR1 is in 18 panels

5 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to green following NHS Genomic Medicine Service approval.
Created: 12 Dec 2025, 3:10 p.m. | Last Modified: 12 Dec 2025, 3:10 p.m.
Panel Version: 6.120
Created: 12 Dec 2025, 3:10 p.m.
Last Modified: 12 Dec 2025, 3:10 p.m.
Panel version: 6.120

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

There is sufficient evidence to promote this gene to Green at the next GMS panel update, inline with the recent review by the R21 Clinical Oversight Group.
Created: 5 Sep 2025, 4:41 p.m. | Last Modified: 5 Sep 2025, 4:41 p.m.
Panel Version: 6.29
Created: 5 Sep 2025, 4:41 p.m.
Last Modified: 5 Sep 2025, 4:41 p.m.
Panel version: 6.29

Natalie Canham (Liverpool Women's Hospital)

Green List (high evidence)

This gene and phenotype were reviewed during meetings in June & July 2025. The meetings included representatives of the North Thames and Central & South R21 testing GLHs and from the R21 Clinical Oversight Group. Clinical review and curation was performed by Natalie Chandler & Elizabeth Scotchman (North Thames GLH), Natalie Bibb, Stephanie Allen & Sarah Graham (Central & South GLH) and Alice Gardham, Esther Kinning, Vicki Harrison, Anna DeBurca, Natalie Canham, Elizabeth Wall, Sunayna Best, Soo-Mi Park & Sahar Mansour (R21 Clinical Oversight Group).
Created: 5 Sep 2025, 4:31 p.m. | Last Modified: 5 Sep 2025, 4:31 p.m.
Panel Version: 6.28
cannot access paper. OMIM report - 19 individuals, 14 famlies, states onset in utero, structural anomalies (polydactyly, simplified gyral pattern, arthrogryposis). Will need to have some caution as also (separately) causes RP
Created: 5 Sep 2025, 2:55 p.m. | Last Modified: 5 Sep 2025, 2:55 p.m.
Panel Version: 6.24

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, OMIM:621060

Publications

Created: 5 Sep 2025, 2:55 p.m.
Last Modified: 5 Sep 2025, 2:55 p.m.
Panel version: 6.28

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Promoting this gene to amber with a recommendation for green rating following GMS review.
Created: 14 Jul 2025, 8:11 p.m. | Last Modified: 14 Jul 2025, 8:11 p.m.
Panel Version: 6.7
Associated with Neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, OMIM:621060.

Variants in this gene have been previously associated with a progressive Retinopathy-sensory neuropathy syndrome, OMIM:609033

PMID: 39306721 - Calame et al 2025 report 27 individuals from 20 families with homozygous/compound het variants in this gene (mainly missense, but also nonsense, frameshift and splice variants). 2 families from S Asia share the same variant and haplotype so could be a founder variant in the region.

13/27 individual had profound ID/DD. 3 were stillborn, and 10 others died before the age of 5, including one in the neonatal period. Severe microcephaly (Z score below -3.0) was observed in 12/27 individuals. Epilepsy was reported in 12 individuals, hypotonia in 17, spasticity in 9 (from 6 families), reduced brain volume in 19 , craniofacial malformations in 4 (those that were still born or died in neonatal period), and limb malformations in 7. An eye phenotype (Cortical visual impairment, Optic disk atrophy or Retinitis pigmentosa) was observed in 15 individuals.

All pathogenic FLVCR1 variants were rare and absent in the homozygous state in gnomAD v2.1.13. Functional studies show that pathogenic FLVCR1 missense variants primarily lie within transmembrane domains and reduce choline and ethanolamine transport activity compared with wild-type FLVCR1.

There are more than 3 cases reported with plausible disease causing variants in more than 3 cases for the intellectual disability, epilepsy, severe microcephaly, limb disorders, fetal anomalies and childhood onset hereditary spastic paraplegia panels. The gene will also be included in the Hypotonic infant superpanel through the inclusion on the Intellectual disability panel.
Created: 14 Jul 2025, 8:09 p.m. | Last Modified: 14 Jul 2025, 8:09 p.m.
Panel Version: 6.6

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, OMIM:621060; neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, MONDO:0976126

Publications

Created: 14 Jul 2025, 8:09 p.m.
Last Modified: 14 Jul 2025, 8:09 p.m.
Panel version: 6.6

Rebecca Foulger (Genomics England curator)

Red List (low evidence)

This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Action taken: Demoted FLVCR1 gene rating from Green to Red.
Created: 24 Mar 2019, 4:30 p.m.
DDG2P rating in original PAGE list: Confirmed for ATAXIA, POSTERIOR COLUMN, WITH RETINITIS PIGMENTOSA
Created: 11 Dec 2018, 9:04 a.m.
In the original PAGE file, MOP listed as All missense/in frame.
Created: 8 Nov 2018, 4:45 p.m.

Mode of pathogenicity
Other - please provide details in the comments

Created: 8 Nov 2018, 4:45 p.m.

Panel version: 0.134

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • Expert Review Green
  • PAGE DD-Gene2Phenotype
Phenotypes
  • Neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, OMIM:621060
  • neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, MONDO:0976126
OMIM
609144
Clinvar variants
Variants in FLVCR1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

16 Dec 2025, Gel status: 3

Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q3_25_promote_green was removed from gene: FLVCR1.

12 Dec 2025, Gel status: 3

Added New Source, Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to FLVCR1. Source NHS GMS was added to FLVCR1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

5 Sep 2025, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Added phenotypes Neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, OMIM:621060 for gene: FLVCR1

14 Jul 2025, Gel status: 2

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for gene: FLVCR1 were changed from ATAXIA, POSTERIOR COLUMN, WITH RETINITIS PIGMENTOSA to Neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, OMIM:621060; neurodevelopmental disorder with microcephaly, absent speech, and hypotonia, MONDO:0976126

14 Jul 2025, Gel status: 2

Set publications

Eleanor Williams (Genomics England Curator)

Publications for gene: FLVCR1 were set to

14 Jul 2025, Gel status: 2

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: flvcr1 has been classified as Amber List (Moderate Evidence).

14 Jul 2025, Gel status: 1

Added Tag

Eleanor Williams (Genomics England Curator)

Tag Q3_25_promote_green tag was added to gene: FLVCR1.

24 Mar 2019, Gel status: 1

Added New Source, Status Update

Rebecca Foulger (Genomics England curator)

Source Expert Review Red was added to FLVCR1. Rating Changed from Green List (high evidence) to Red List (low evidence)

8 Nov 2018, Gel status: 4

Created, Added New Source, Set mode of inheritance, Set Phenotypes

Rebecca Foulger (Genomics England curator)

gene: FLVCR1 was added gene: FLVCR1 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: FLVCR1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: FLVCR1 were set to ATAXIA, POSTERIOR COLUMN, WITH RETINITIS PIGMENTOSA