LNX2

ligand of numb-protein X 2, the group of Ring finger proteins|PDZ domain containing

Basic information

Region (hg38): 13:27545912-27620529

Previous symbols: [ "PDZRN1" ]

Links

ENSG00000139517 ∙ ∙ OMIM:609733 ∙ HGNC:20421 ∙ Uniprot:Q8N448 ∙ 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 LNX2 gene.

• Inborn genetic diseases (26 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LNX2 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					1	1
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	1

Variants in LNX2

This is a list of pathogenic ClinVar variants found in the LNX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-27548406-C-T		not specified	Uncertain significance (Feb 13, 2024)
13-27548409-G-C		not specified	Uncertain significance (Mar 06, 2023)
13-27548420-C-T		not specified	Uncertain significance (Aug 02, 2023)
13-27548423-A-C		not specified	Uncertain significance (Nov 17, 2023)
13-27550343-C-T		not specified	Uncertain significance (Apr 25, 2023)
13-27550433-A-G		not specified	Uncertain significance (Dec 13, 2022)
13-27553252-A-C		not specified	Uncertain significance (Sep 19, 2023)
13-27556239-T-C		not specified	Uncertain significance (Mar 23, 2023)
13-27556336-G-A			Benign (Apr 04, 2018)
13-27556343-C-T		not specified	Uncertain significance (Mar 27, 2023)
13-27559847-G-A		not specified	Uncertain significance (Jan 26, 2023)
13-27559921-A-G		not specified	Uncertain significance (Feb 01, 2023)
13-27559960-G-A		not specified	Uncertain significance (May 09, 2023)
13-27559961-T-C		not specified	Uncertain significance (Jul 12, 2023)
13-27562414-T-C		not specified	Uncertain significance (Sep 27, 2022)
13-27562458-G-T		not specified	Uncertain significance (Feb 11, 2022)
13-27562472-C-T		not specified	Uncertain significance (Jul 15, 2021)
13-27562486-T-C		not specified	Uncertain significance (Dec 18, 2023)
13-27562496-G-C		not specified	Uncertain significance (Jan 04, 2024)
13-27562523-C-A		not specified	Uncertain significance (Aug 29, 2022)
13-27562557-A-C		not specified	Uncertain significance (Dec 14, 2022)
13-27562678-A-C		not specified	Uncertain significance (Jan 17, 2023)
13-27562681-C-T		not specified	Uncertain significance (Nov 15, 2021)
13-27562724-G-C		not specified	Uncertain significance (Dec 20, 2023)
13-27562759-T-C		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LNX2	protein_coding	protein_coding	ENST00000316334	9	74492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000731	0.999	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.706	342	381	0.898	0.0000200	4512
Missense in Polyphen		128	185.08	0.6916		2188
Synonymous	-0.0901	151	150	1.01	0.00000859	1377
Loss of Function	2.91	14	31.7	0.442	0.00000204	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000218	0.000217
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.629
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.199
• hipred: Y
• hipred_score: 0.756
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.922

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lnx2

Zebrafish Information Network

• Gene name: lnx2a
• Affected structure: anterior pancreatic bud
• Phenotype tag: abnormal
• Phenotype quality: decreased process quality

Gene ontology

• Molecular function: protein binding;metal ion binding