PLXNC1

plexin C1, the group of CD molecules|Plexins|IPT domain containing

Basic information

Region (hg38): 12:94148577-94307675

Links

ENSG00000136040 ∙ NCBI:10154 ∙ OMIM:604259 ∙ HGNC:9106 ∙ Uniprot:O60486 ∙ 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 PLXNC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLXNC1 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				4	1	5
missense			69	11	2	82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region			1	1	3	5
non coding			1	1		2
Total	0	0	70	16	4

Variants in PLXNC1

This is a list of pathogenic ClinVar variants found in the PLXNC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-94148982-C-T		not specified	Uncertain significance (Feb 27, 2024)
12-94148997-C-T		not specified	Uncertain significance (Dec 02, 2022)
12-94149008-C-A		not specified	Uncertain significance (Feb 07, 2023)
12-94149021-C-G		not specified	Uncertain significance (May 31, 2023)
12-94149194-A-C		not specified	Likely benign (Apr 07, 2023)
12-94149196-C-G		not specified	Likely benign (Apr 07, 2023)
12-94149212-C-G		not specified	Uncertain significance (Oct 13, 2023)
12-94149229-C-G		not specified	Uncertain significance (Jul 15, 2021)
12-94149245-T-C		not specified	Uncertain significance (Apr 07, 2023)
12-94149251-G-A		not specified	Uncertain significance (Apr 07, 2023)
12-94149321-C-T		not specified	Uncertain significance (Oct 16, 2023)
12-94149402-G-A		not specified	Uncertain significance (Apr 23, 2024)
12-94149467-G-A		not specified	Uncertain significance (Aug 09, 2021)
12-94149476-G-A		not specified	Uncertain significance (Sep 06, 2022)
12-94149483-G-C		not specified	Uncertain significance (Apr 07, 2023)
12-94149485-A-C		not specified	Uncertain significance (Apr 07, 2023)
12-94149487-C-G		not specified	Uncertain significance (Apr 07, 2023)
12-94149573-A-G		not specified	Likely benign (Apr 07, 2023)
12-94149576-A-G		not specified	Uncertain significance (Apr 07, 2023)
12-94149577-C-A		not specified	Uncertain significance (Apr 07, 2023)
12-94149579-C-T		not specified	Uncertain significance (Apr 07, 2023)
12-94149642-A-G		not specified	Uncertain significance (Apr 07, 2023)
12-94149647-T-C		not specified	Likely benign (Apr 07, 2023)
12-94149657-C-G		not specified	Uncertain significance (Apr 07, 2023)
12-94149695-G-C		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLXNC1	protein_coding	protein_coding	ENST00000258526	31	158953

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00189	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.98	505	828	0.610	0.0000434	10198
Missense in Polyphen		134	310.62	0.43139		4049
Synonymous	0.176	331	335	0.988	0.0000191	3002
Loss of Function	6.67	13	75.6	0.172	0.00000352	952

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000243
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000110	0.000109
South Asian	0.0000985	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for SEMA7A, for smallpox semaphorin A39R, vaccinia virus semaphorin A39R and for herpesvirus Sema protein. Binding of semaphorins triggers cellular responses leading to the rearrangement of the cytoskeleton and to secretion of IL6 and IL8 (By similarity). {ECO:0000250, ECO:0000269|PubMed:20727575}.
• Pathway: Axon guidance - Homo sapiens (human);Developmental Biology;Other semaphorin interactions;Semaphorin interactions;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.304
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.92

Haploinsufficiency Scores

• pHI: 0.696
• hipred: Y
• hipred_score: 0.581
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.247

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plxnc1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype; cellular phenotype

Gene ontology

• Biological process: cell adhesion;negative regulation of cell adhesion;regulation of cell shape;regulation of cell migration;regulation of GTPase activity;positive regulation of axonogenesis;semaphorin-plexin signaling pathway involved in axon guidance
• Cellular component: semaphorin receptor complex;plasma membrane;integral component of plasma membrane;membrane
• Molecular function: signaling receptor binding;protein binding;semaphorin receptor activity