CNKSR3

CNKSR family member 3, the group of PDZ domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 6:154387515-154510685

Previous symbols: [ "MAGI1" ]

Links

ENSG00000153721 ∙ NCBI:154043 ∙ OMIM:617476 ∙ HGNC:23034 ∙ Uniprot:Q6P9H4 ∙ 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 CNKSR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNKSR3 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					2	2
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			1			1
Total	0	0	31	0	2

Variants in CNKSR3

This is a list of pathogenic ClinVar variants found in the CNKSR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-154406439-G-A		not specified	Uncertain significance (Feb 10, 2023)
6-154406465-G-T		not specified	Uncertain significance (Aug 05, 2024)
6-154406472-A-T		not specified	Uncertain significance (Aug 08, 2023)
6-154406535-C-T		not specified	Uncertain significance (Jul 20, 2021)
6-154406547-T-A		not specified	Uncertain significance (Feb 27, 2023)
6-154406574-C-G		not specified	Uncertain significance (Oct 10, 2023)
6-154406607-G-A		not specified	Uncertain significance (Jan 02, 2024)
6-154406611-G-A		not specified	Uncertain significance (Oct 22, 2021)
6-154406621-G-C		not specified	Uncertain significance (Sep 20, 2023)
6-154410357-C-T		not specified	Uncertain significance (Aug 28, 2023)
6-154410369-G-A		not specified	Uncertain significance (Jul 22, 2024)
6-154410382-C-T		not specified	Uncertain significance (Nov 25, 2024)
6-154410412-T-C		not specified	Uncertain significance (Dec 04, 2024)
6-154410432-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-154411062-G-A		not specified	Uncertain significance (Nov 08, 2024)
6-154411062-G-C		not specified	Uncertain significance (Oct 26, 2022)
6-154411075-C-T		not specified	Uncertain significance (Feb 13, 2024)
6-154411125-A-G		not specified	Uncertain significance (Feb 27, 2023)
6-154414300-G-A		not specified	Uncertain significance (Mar 30, 2024)
6-154414346-G-C		not specified	Uncertain significance (Nov 10, 2022)
6-154414407-G-A		not specified	Uncertain significance (Oct 04, 2022)
6-154422573-G-A		not specified	Uncertain significance (Aug 07, 2024)
6-154422577-G-A		not specified	Uncertain significance (Sep 16, 2021)
6-154422597-A-G		not specified	Uncertain significance (Jan 16, 2024)
6-154428184-T-C		not specified	Uncertain significance (Jun 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNKSR3	protein_coding	protein_coding	ENST00000607772	13	123156

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0282	0.972	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.585	301	331	0.909	0.0000199	3576
Missense in Polyphen		111	133.37	0.83225		1418
Synonymous	0.965	120	134	0.894	0.00000837	1109
Loss of Function	3.74	9	31.8	0.283	0.00000187	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000274	0.000274
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000282	0.000277
European (Non-Finnish)	0.000174	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.000231	0.000229
Other	0.000338	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transepithelial sodium transport. Regulates aldosterone-induced and epithelial sodium channel (ENaC)-mediated sodium transport through regulation of ENaC cell surface expression. Acts as a scaffold protein coordinating the assembly of an ENaC-regulatory complex (ERC). {ECO:0000269|PubMed:22851176}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.619
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.15

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.270
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnksr3

Gene ontology

• Biological process: positive regulation of sodium ion transport;negative regulation of peptidyl-serine phosphorylation;negative regulation of ERK1 and ERK2 cascade;positive regulation of sodium ion transmembrane transporter activity
• Cellular component: cytoplasm;apical plasma membrane
• Molecular function: protein binding