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Fetal anomalies

STR: CNBP_CCTG

Red List (low evidence)
Chromosome: 3
GRCh37 Position: 128891420-128891499
GRCh38 Position: 129172577-129172656
Repeated Sequence: CCTG
Normal Number of Repeats: < 27
Pathogenic Number of Repeats: = or > 75

CNBP (CCHC-type zinc finger nucleic acid binding protein)
EnsemblGeneIds (GRCh38): ENSG00000169714
EnsemblGeneIds (GRCh37): ENSG00000169714
OMIM: 116955, Gene2Phenotype
CNBP is in 0 panels

4 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

I don't know

The repeated sequence of this STR has been updated from 'CAGG' to 'CCTG' to match the sequence on the coding strand of the gene. This update was made following NHS Genomic Medicine Service approval.
Created: 10 Mar 2025, 11:16 a.m. | Last Modified: 10 Mar 2025, 11:16 a.m.
Panel Version: 5.79
After NHS Genomic Medicine Service consideration, the rating of this gene has not been changed and remains amber. The reviewers note that R21 analysis does not currently include STRs.
Created: 25 Feb 2025, 3:40 p.m. | Last Modified: 25 Feb 2025, 3:40 p.m.
Panel Version: 5.78
Created: 25 Feb 2025, 3:40 p.m.
Last Modified: 25 Feb 2025, 3:40 p.m.
Panel version: 5.79

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

As STR: CNBP_CCTG has been reviewed and confirmed by the NHS Genomic Medicine Service, it can be rated as Green on this panel.
Created: 23 Jan 2024, 2:48 p.m. | Last Modified: 23 Jan 2024, 2:48 p.m.
Panel Version: 3.124
Created: 23 Jan 2024, 2:48 p.m.
Last Modified: 23 Jan 2024, 2:48 p.m.
Panel version: 3.124

Eleanor Williams (Genomics England Curator)

STR repeat lengths have been reviewed and confirmed by the NHS Genomic Medicine Service.
Created: 15 Mar 2022, 12:52 p.m. | Last Modified: 15 Mar 2022, 12:52 p.m.
Panel Version: 1.842
Created: 15 Mar 2022, 12:52 p.m.
Last Modified: 15 Mar 2022, 12:52 p.m.
Panel version: 1.842

Arina Puzriakova (Genomics England Curator)

Red List (low evidence)

Comment on list classification: This STR was downgraded from Amber to Red inline with the Red review by the R21 Clinical Oversight Group.
Created: 5 Sep 2025, 3:40 p.m. | Last Modified: 5 Sep 2025, 3:40 p.m.
Panel Version: 6.25
This STR 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, 3:11 p.m. | Last Modified: 5 Sep 2025, 3:11 p.m.
Panel Version: 6.24
Red expert review added on behalf of Alice Gardham (North West Thames Genetics), as part of a review of this panel by the R21 Clinical Oversight Group:

"Myotonic dytrophy 2 - no fetal presentation."
Created: 5 Sep 2025, 3 p.m. | Last Modified: 5 Sep 2025, 3 p.m.
Panel Version: 6.24
Comment on list classification: There is enough evidence to support the gene-disease association but setting rating to Red as currently the performance of the pipeline for this STR is very poor as it is located in a complex locus.
Created: 9 Nov 2021, 1:43 p.m. | Last Modified: 9 Nov 2021, 1:43 p.m.
Panel Version: 1.803
The mutation is a CCTG repeat expansion in intron 1 of the CNBP (ZNF9) gene. The range of expanded allele sizes is 75 to 11,000 CCTG repeats, whereas normal is up to 30.

The CCTG repeat tract in normal alleles typically contains one or more tetranucleotide interruptions. The sequence interruptions that are routinely found within the CCTG tracts of normal alleles are not found in sequenced pathogenic CCTG expansions of CNBP alleles. On transmission to the next generation, CNBP repeat length sometimes diminishes dramatically, without significant differences determined by the gender of the transmitting parent.
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Copied from Rhiannon Mellis (GOSH) review of gene CNBP on Fetal anomalies panel:

This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene.
Sources: Expert Review
Created: 9 Nov 2021, 1:40 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Myotonic dystrophy 2, OMIM:602668

Created: 9 Nov 2021, 1:40 p.m.
Last Modified: 5 Sep 2025, 3 p.m.
Panel version: 6.24

Details

Name
CNBP_CCTG
Chromosome
3
GRCh37 Coordinates
128891420-128891499
GRCh38 Coordinates
129172577-129172656
Repeated Sequence
CCTG
Normal Number of Repeats: <
27
Pathogenic Number of Repeats: = or >
75
Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Red
  • NHS GMS
  • Expert Review
Phenotypes
  • Myotonic dystrophy 2, OMIM:602668
Tags
STR
OMIM
116955
Clinvar variants
Variants in CNBP
Penetrance
None

History Filter Activity

5 Sep 2025, Gel status: 1

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Str: cnbp_cctg has been classified as Red List (Low Evidence).

5 Sep 2025, Gel status: 1

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Str: cnbp_cctg has been classified as Red List (Low Evidence).

10 Mar 2025, Gel status: 2

Changed Repeated Sequence

Achchuthan Shanmugasundram (Genomics England Curator)

Repeated Sequence for CNBP_CCTG was changed from CAGG to CCTG.

25 Feb 2025, Gel status: 2

Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q1_24_promote_green was removed from STR: CNBP_CCTG.

23 Jan 2024, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Str: cnbp_cctg has been classified as Amber List (Moderate Evidence).

23 Jan 2024, Gel status: 1

Removed Tag, Added Tag

Sarah Leigh (Genomics England Curator)

Tag NGS Not Validated was removed from STR: CNBP_CCTG. Tag Q1_24_promote_green tag was added to STR: CNBP_CCTG.

10 Mar 2022, Gel status: 1

Changed Normal Number of Repeats, Added New Source

Arina Puzriakova (Genomics England Curator)

Normal Number of Repeats for CNBP_CCTG was changed from 26 to 27. Source NHS GMS was added to STR: CNBP_CCTG.

9 Nov 2021, Gel status: 1

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Str: cnbp_cctg has been classified as Red List (Low Evidence).

9 Nov 2021, Gel status: 1

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

Arina Puzriakova (Genomics England Curator)

STR: CNBP_CCTG was added STR: CNBP_CCTG was added to Fetal anomalies. Sources: Expert Review STR, NGS Not Validated tags were added to STR: CNBP_CCTG. Mode of inheritance for STR: CNBP_CCTG was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for STR: CNBP_CCTG were set to Myotonic dystrophy 2, OMIM:602668