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Intellectual disability

Gene: LONP1

Green List (high evidence)
LONP1 (lon peptidase 1, mitochondrial)
EnsemblGeneIds (GRCh38): ENSG00000196365
EnsemblGeneIds (GRCh37): ENSG00000196365
OMIM: 605490, Gene2Phenotype
LONP1 is in 11 panels

7 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on mode of inheritance: There are at least three unrelated individuals reported with monoallelic LONP1 variants and syndromic intellectual disability. Hence, the MOI for this gene can be updated to 'BOTH monoallelic and biallelic, autosomal or pseudoautosomal' in the next GMS update.
Created: 23 Jul 2026, 2:14 p.m. | Last Modified: 23 Jul 2026, 2:14 p.m.
Panel Version: 10.57
PMID:40931319 (2026) reported 16 individuals with 16 different variants in LONP1 gene, of which 11 individuals are new patients with neurodevelopmental features without congenital diaphragmatic hernia (CDH) or classic cerebral, Ocular, Dental, Auricular, and Skeletal anomalies syndrome (CODAS features), and five are previously reported cases. Seven of these patients are identified with heterozygous variants, while the rest are identified with either homozygous or compound heterozygous variants. Developmental delay was reported in all seven monoallelic cases and six biallelic cases, while intellectual disability was reported in three monoallelic cases and six biallelic cases (mild in one).

Biallelic variants are associated with relevant phenotypes in OMIM (MIM #600373, last accessed 23 July 2026) and in Gene2Phenotype ('strong' rating on DD, Eye and Skeletal panels). Monoallelic variants are not yet associated with relevant phenotypes in OMIM.
Created: 23 Jul 2026, 2:07 p.m. | Last Modified: 23 Jul 2026, 2:07 p.m.
Panel Version: 10.55

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
CODAS syndrome, OMIM:600373; CODAS syndrome, MONDO:0010879; neurodevelopmental disorder, MONDO:0700092

Publications

Created: 23 Jul 2026, 2:07 p.m.
Last Modified: 23 Jul 2026, 2:07 p.m.
Panel version: 10.56

Louise Daugherty (Genomics England Curator)

Comment on publications: added more publications to support the phenotype
Created: 14 Mar 2018, 1:18 p.m.
Created: 14 Mar 2018, 1:18 p.m.

Panel version: 2.24

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Sufficient number of cases from a range of ethnic backgrounds with different variants and an appropriate phenotype.
Created: 8 Mar 2018, 3 p.m.
Comment on list classification: In OMIM developmental delay is a fairly consistently reported feature (all 5 papers comprising the clinical features section refer to psychomotor delay, developmental delay, functioning at a level lower than expected).
Created: 8 Mar 2018, 2:59 p.m.
Created: 8 Mar 2018, 2:59 p.m.

Panel version: Imported from Intellectual disability update Jan 2018 panel version 0.456

Sarah Leigh (Genomics England Curator)

Associated with phenotype in OMIM and as a probable G2P association. At least 4 homozygous or compound-heterozygous variants were identified in 10 cases from 3 different ancestral backgrounds, a part of the variable phenotype, intellectual disability was associated with 2 variants from 2 different ancestral backgrounds.
Created: 8 Mar 2018, 1:44 p.m.
Created: 8 Mar 2018, 1:44 p.m.

Panel version: Imported from Intellectual disability update Jan 2018 panel version 0.442

Caroline Wright (Sanger)

I don't know

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
CODAS SYNDROME

Publications

Created: 5 Nov 2017, 2:42 a.m.

Panel version: 0

Lu Raymond (university of cambridge )

I don't know

Created: 23 Feb 2016, 10:07 a.m.

Panel version: 0.306

Richard Scott (Genomics England Curator)

Comment on list classification: 3 ancestral allele pairs reported to date. Further evidence required before diagnostic
Created: 7 Feb 2016, 10:59 p.m.
Created: 7 Feb 2016, 10:59 p.m.

Panel version: 0.171

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Expert Review Green
Phenotypes
  • CODAS syndrome, OMIM:600373
  • CODAS syndrome, MONDO:0010879
  • neurodevelopmental disorder, MONDO:0700092
Tags
Q3_26_MOI
OMIM
605490
Clinvar variants
Variants in LONP1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

23 Jul 2026, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: LONP1 were changed from CODAS syndrome, 600373; Cerebral, ocular, dental, auricular, and skeletal anomalies syndrome to CODAS syndrome, OMIM:600373; CODAS syndrome, MONDO:0010879; neurodevelopmental disorder, MONDO:0700092

23 Jul 2026, Gel status: 3

Set mode of inheritance

Achchuthan Shanmugasundram (Genomics England Curator)

Mode of inheritance for gene: LONP1 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

23 Jul 2026, Gel status: 3

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: LONP1 were set to 25574826; 20503327; 11471171; 1887855

23 Jul 2026, Gel status: 3

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q3_26_MOI tag was added to gene: LONP1.

11 Feb 2021, Gel status: 3

Clear Sources

Ivone Leong (Genomics England Curator)

Source: Expert Review Red was removed from gene: LONP1

14 Mar 2018, Gel status: 4

Set publications

Louise Daugherty (Genomics England Curator)

Publications for LONP1 were set to 25574826; 20503327; 11471171; 1887855

14 Mar 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for LONP1 were set to CODAS syndrome, 600373; Cerebral, ocular, dental, auricular, and skeletal anomalies syndrome

12 Mar 2018, Gel status: 4

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

12 Mar 2018, Gel status: 4

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Green was added to LONP1. Panel: Intellectual disability Publications for gene LONP1 was set to ['25574826', '20503327']

7 Feb 2016, Gel status: 1

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

7 Feb 2016, Gel status: 1

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 0

Created

Ellen McDonagh (Genomics England Curator)

LONP1 was created by ellenmcdonagh

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

LONP1 was added to Intellectual disabilitypanel. Sources: Expert Review Amber