FMOD

fibromodulin, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 1:203340628-203351758

Links

ENSG00000122176 ∙ NCBI:2331 ∙ OMIM:600245 ∙ HGNC:3774 ∙ Uniprot:Q06828 ∙ 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 FMOD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FMOD 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			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in FMOD

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

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

Position	Type	Phenotype	Significance	ClinVar
1-203342414-C-G		not specified	Uncertain significance (May 31, 2023)
1-203347295-T-G		not specified	Uncertain significance (Aug 21, 2023)
1-203347379-G-T		not specified	Uncertain significance (Oct 25, 2023)
1-203347436-T-C		not specified	Uncertain significance (Dec 19, 2022)
1-203347450-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-203347472-C-G		not specified	Uncertain significance (Dec 01, 2022)
1-203347490-C-T		not specified	Uncertain significance (May 20, 2024)
1-203347496-C-T		not specified	Uncertain significance (Oct 29, 2021)
1-203347523-A-G		not specified	Uncertain significance (Nov 03, 2022)
1-203347556-G-T		not specified	Uncertain significance (Aug 31, 2022)
1-203347564-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-203347595-T-C		not specified	Uncertain significance (Apr 23, 2024)
1-203347604-G-A		not specified	Uncertain significance (May 04, 2023)
1-203347702-C-T		not specified	Uncertain significance (Aug 19, 2023)
1-203347744-C-T		not specified	Uncertain significance (Jun 28, 2023)
1-203347823-C-G		not specified	Uncertain significance (May 02, 2024)
1-203347832-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-203347834-A-G		not specified	Uncertain significance (Jun 24, 2022)
1-203347854-G-T		not specified	Uncertain significance (Nov 19, 2022)
1-203347859-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-203347872-C-G		not specified	Uncertain significance (Jan 16, 2024)
1-203347901-C-T		not specified	Uncertain significance (Dec 17, 2023)
1-203347979-T-G		not specified	Uncertain significance (Jun 06, 2023)
1-203348000-A-G		not specified	Uncertain significance (Jan 16, 2024)
1-203348030-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FMOD	protein_coding	protein_coding	ENST00000354955	2	10862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00236	0.932	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0844	228	224	1.02	0.0000140	2460
Missense in Polyphen		72	79.813	0.90211		998
Synonymous	0.387	99	104	0.952	0.00000668	776
Loss of Function	1.61	6	12.0	0.499	5.85e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000679	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Affects the rate of fibrils formation. May have a primary role in collagen fibrillogenesis (By similarity). {ECO:0000250}.
• Pathway: Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Extracellular matrix organization;Metabolism;ECM proteoglycans (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.378
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.307
• hipred: N
• hipred_score: 0.398
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.752

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fmod
• Phenotype: skeleton phenotype; immune system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; craniofacial phenotype; muscle phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: transforming growth factor beta receptor complex assembly;keratan sulfate biosynthetic process;collagen fibril organization;keratan sulfate catabolic process
• Cellular component: extracellular region;extracellular space;Golgi lumen;extracellular matrix;lysosomal lumen;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent conferring compression resistance