FREM3

FRAS1 related extracellular matrix 3

Basic information

Region (hg38): 4:143577301-143700675

Links

ENSG00000183090 ∙ NCBI:166752 ∙ OMIM:608946 ∙ HGNC:25172 ∙ Uniprot:P0C091 ∙ 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 FREM3 gene.

• Inborn genetic diseases (105 variants)
• not provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FREM3 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				6	2	8
missense			99	6	1	106
nonsense			1			1
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	101	12	3

Variants in FREM3

This is a list of pathogenic ClinVar variants found in the FREM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-143577708-G-A		not specified	Uncertain significance (Jan 30, 2024)
4-143577773-G-C		not specified	Uncertain significance (Sep 06, 2022)
4-143577792-T-C		not specified	Uncertain significance (May 16, 2023)
4-143577798-C-A		not specified	Uncertain significance (Jan 23, 2024)
4-143577798-C-T		not specified	Likely benign (Mar 24, 2023)
4-143585865-A-C		not specified	Uncertain significance (Apr 13, 2022)
4-143585876-C-T		not specified	Likely benign (Jun 23, 2023)
4-143585880-C-T			Benign (Jun 13, 2018)
4-143585883-C-T		not specified	Likely benign (Apr 19, 2023)
4-143585942-C-T		not specified	Uncertain significance (Jan 16, 2024)
4-143611288-G-A		not specified	Uncertain significance (Jan 24, 2024)
4-143611313-G-A			Likely benign (Mar 01, 2023)
4-143611320-A-T		not specified	Uncertain significance (Jun 06, 2023)
4-143611384-C-T		not specified	Uncertain significance (Sep 26, 2023)
4-143611434-T-C		not specified	Uncertain significance (Mar 07, 2024)
4-143611507-A-C		not specified	Uncertain significance (Apr 20, 2023)
4-143621043-G-A		not specified	Uncertain significance (Apr 17, 2023)
4-143621088-G-A			Uncertain significance (Feb 02, 2016)
4-143624236-C-A		not specified	Uncertain significance (Dec 15, 2023)
4-143624269-T-C		not specified	Uncertain significance (Sep 14, 2022)
4-143627635-G-A		not specified	Uncertain significance (Jul 30, 2023)
4-143693146-T-C		not specified	Uncertain significance (Jan 06, 2023)
4-143695505-C-T		not specified	Uncertain significance (Dec 14, 2021)
4-143695551-C-G		not specified	Uncertain significance (Apr 19, 2023)
4-143695586-T-G		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FREM3	protein_coding	protein_coding	ENST00000329798	8	123374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-19	0.875	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.97	843	1.12e+3	0.751	0.0000565	13988
Missense in Polyphen		156	241.06	0.64714		3203
Synonymous	4.42	335	455	0.736	0.0000240	4404
Loss of Function	2.31	39	58.0	0.672	0.00000298	707

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Extracellular matrix protein which may play a role in cell adhesion. {ECO:0000250}.

Recessive Scores

• pRec: 0.0987

Intolerance Scores

• rvis_EVS: 4.07
• rvis_percentile_EVS: 99.68

Haploinsufficiency Scores

• pHI: 0.144

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.103

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frem3

Gene ontology

• Biological process: cell communication;cell adhesion
• Cellular component: basement membrane;extracellular space;integral component of membrane;collagen-containing extracellular matrix
• Molecular function: metal ion binding