CLRN3

clarin 3, the group of Clarins

Basic information

Region (hg38): 10:127877840-127892941

Previous symbols: [ "TMEM12" ]

Links

ENSG00000180745 ∙ NCBI:119467 ∙ OMIM:620256 ∙ HGNC:20795 ∙ Uniprot:Q8NCR9 ∙ 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 CLRN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLRN3 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			17	3		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	0

Variants in CLRN3

This is a list of pathogenic ClinVar variants found in the CLRN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-127878207-C-T		not specified	Likely benign (Oct 05, 2022)
10-127878243-G-T		not specified	Uncertain significance (Mar 14, 2023)
10-127878247-C-T		not specified	Uncertain significance (Jan 31, 2024)
10-127878271-C-T		not specified	Likely benign (Nov 07, 2022)
10-127878312-G-A		not specified	Uncertain significance (May 01, 2022)
10-127878358-C-T		not specified	Uncertain significance (Apr 13, 2022)
10-127878378-G-A		not specified	Uncertain significance (Apr 04, 2023)
10-127878384-G-T		not specified	Uncertain significance (Nov 18, 2022)
10-127878385-C-T		not specified	Uncertain significance (Nov 18, 2022)
10-127883698-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-127883713-G-A		not specified	Uncertain significance (May 09, 2023)
10-127883725-G-A		not specified	Likely benign (Nov 09, 2021)
10-127883728-G-A		not specified	Uncertain significance (Mar 25, 2024)
10-127883757-G-C		not specified	Uncertain significance (Jul 14, 2021)
10-127883800-A-G		not specified	Uncertain significance (Feb 13, 2024)
10-127883836-T-C		not specified	Uncertain significance (Apr 07, 2022)
10-127883872-A-G		not specified	Uncertain significance (Jul 09, 2021)
10-127892564-T-A		not specified	Uncertain significance (Jan 26, 2022)
10-127892693-T-G		not specified	Uncertain significance (Apr 06, 2023)
10-127892703-G-C		not specified	Uncertain significance (Jun 09, 2022)
10-127892770-C-A		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLRN3	protein_coding	protein_coding	ENST00000368671	3	15107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0392	0.850	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.538	144	127	1.13	0.00000739	1469
Missense in Polyphen		42	41.352	1.0157		509
Synonymous	0.113	56	57.1	0.981	0.00000417	453
Loss of Function	1.29	3	6.56	0.458	2.80e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000598	0.000598
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0884

Intolerance Scores

• loftool: 0.478
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• pHI: 0.0433
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0182

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clrn3

Gene ontology

• Cellular component: integral component of membrane;extracellular exosome