MORN3

MORN repeat containing 3

Basic information

Region (hg38): 12:121648742-121672631

Links

ENSG00000139714 ∙ NCBI:283385 ∙ ∙ HGNC:29807 ∙ Uniprot:Q6PF18 ∙ 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 MORN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MORN3 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			24	3	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	24	3	1

Variants in MORN3

This is a list of pathogenic ClinVar variants found in the MORN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-121652742-C-T		not specified	Uncertain significance (Apr 12, 2022)
12-121653094-G-A		not specified	Uncertain significance (Nov 07, 2023)
12-121653110-C-T		not specified	Uncertain significance (Dec 21, 2023)
12-121653115-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-121653116-G-A		not specified	Uncertain significance (Dec 18, 2023)
12-121653125-C-T		not specified	Uncertain significance (Feb 13, 2025)
12-121653133-G-C		not specified	Uncertain significance (Sep 27, 2021)
12-121653145-G-A		not specified	Uncertain significance (Nov 14, 2024)
12-121653179-G-C			Benign (Jul 13, 2018)
12-121653221-T-C		not specified	Uncertain significance (Dec 21, 2023)
12-121653242-C-T		not specified	Uncertain significance (Oct 27, 2022)
12-121653247-C-T		not specified	Uncertain significance (Jan 04, 2024)
12-121653254-C-T		not specified	Uncertain significance (Aug 15, 2023)
12-121653265-G-A			Benign (Jun 27, 2018)
12-121654323-C-G		not specified	Uncertain significance (Sep 13, 2023)
12-121654331-T-C		not specified	Uncertain significance (Mar 19, 2024)
12-121654338-G-C		not specified	Uncertain significance (Jan 09, 2024)
12-121654342-C-A		not specified	Uncertain significance (Dec 21, 2022)
12-121659214-A-G		not specified	Uncertain significance (Apr 10, 2023)
12-121659225-A-C		not specified	Uncertain significance (Oct 04, 2022)
12-121659259-G-C		not specified	Uncertain significance (Sep 21, 2023)
12-121659309-T-C		not specified	Uncertain significance (Nov 17, 2022)
12-121659334-C-T		not specified	Likely benign (Sep 02, 2024)
12-121669344-T-C		not specified	Uncertain significance (Dec 17, 2023)
12-121669351-T-C		not specified	Uncertain significance (Jun 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MORN3	protein_coding	protein_coding	ENST00000355329	5	21514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.54e-7	0.403	125665	0	82	125747	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.616	129	150	0.859	0.00000944	1571
Missense in Polyphen		46	48.734	0.94391		432
Synonymous	0.413	55	59.0	0.932	0.00000428	404
Loss of Function	0.705	12	14.9	0.803	7.23e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000404	0.000394
Ashkenazi Jewish	0.00220	0.00218
East Asian	0.000925	0.000870
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000280	0.000264
Middle Eastern	0.000925	0.000870
South Asian	0.000108	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.725
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.0941
• hipred: N
• hipred_score: 0.204
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.214

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Morn3

Gene ontology

• Cellular component: nucleus
• Molecular function: protein binding