CNST

consortin, connexin sorting protein, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 1:246566444-246668595

Previous symbols: [ "C1orf71" ]

Links

ENSG00000162852 ∙ NCBI:163882 ∙ OMIM:613439 ∙ HGNC:26486 ∙ Uniprot:Q6PJW8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNST gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNST gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			61	3		64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	61	3	0

Variants in CNST

This is a list of pathogenic ClinVar variants found in the CNST region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-246591575-G-A		not specified	Uncertain significance (Nov 13, 2024)
1-246591601-A-G		not specified	Uncertain significance (Feb 07, 2025)
1-246591642-G-A		not specified	Uncertain significance (Jun 30, 2024)
1-246591660-C-T		not specified	Uncertain significance (Mar 23, 2022)
1-246591689-C-T		not specified	Uncertain significance (Oct 29, 2024)
1-246591690-T-C		not specified	Uncertain significance (Mar 07, 2023)
1-246591792-T-G		not specified	Uncertain significance (Dec 14, 2023)
1-246591829-C-A		not specified	Uncertain significance (Aug 02, 2022)
1-246591909-G-A		not specified	Uncertain significance (Jun 11, 2024)
1-246591929-A-C		not specified	Uncertain significance (May 31, 2023)
1-246591930-A-G		not specified	Uncertain significance (May 30, 2024)
1-246621449-G-C		not specified	Uncertain significance (Apr 06, 2022)
1-246621459-T-G		not specified	Uncertain significance (Dec 20, 2021)
1-246621473-C-G		not specified	Uncertain significance (Feb 28, 2025)
1-246621479-G-A		not specified	Uncertain significance (May 10, 2022)
1-246621494-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-246621531-A-T		not specified	Uncertain significance (Apr 14, 2022)
1-246621552-T-C		not specified	Uncertain significance (Mar 07, 2023)
1-246621563-T-C		not specified	Uncertain significance (Aug 10, 2024)
1-246621579-T-C		not specified	Uncertain significance (Jun 11, 2024)
1-246621627-T-A		not specified	Uncertain significance (Jan 29, 2025)
1-246633957-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-246633963-A-G		not specified	Uncertain significance (Aug 04, 2023)
1-246634481-T-C		not specified	Uncertain significance (Apr 24, 2024)
1-246634508-A-T		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNST	protein_coding	protein_coding	ENST00000366513	10	102141

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000124	0.998	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00278	381	381	1.00	0.0000200	4770
Missense in Polyphen		85	106.29	0.79971		1458
Synonymous	-2.01	180	149	1.21	0.00000898	1377
Loss of Function	2.70	15	31.3	0.479	0.00000162	414

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000248	0.000246
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for targeting of connexins to the plasma membrane. {ECO:0000269|PubMed:19864490}.

Recessive Scores

• pRec: 0.0833

Intolerance Scores

• loftool: 0.543
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.82

Haploinsufficiency Scores

• pHI: 0.382
• hipred: N
• hipred_score: 0.316
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cnst

Gene ontology

• Biological process: negative regulation of phosphatase activity;positive regulation of Golgi to plasma membrane protein transport
• Cellular component: trans-Golgi network;plasma membrane;membrane;integral component of membrane;transport vesicle;protein-containing complex;intracellular membrane-bounded organelle
• Molecular function: protein binding;phosphatase binding;connexin binding