FAM3C

FAM3 metabolism regulating signaling molecule C

Basic information

Region (hg38): 7:121348877-121396364

Links

ENSG00000196937 ∙ NCBI:10447 ∙ OMIM:608618 ∙ HGNC:18664 ∙ Uniprot:Q92520 ∙ 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 FAM3C gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM3C 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in FAM3C

This is a list of pathogenic ClinVar variants found in the FAM3C region.

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

Position	Type	Phenotype	Significance	ClinVar
7-121350538-T-C		not specified	Uncertain significance (Aug 02, 2021)
7-121351165-T-C		not specified	Uncertain significance (Dec 08, 2021)
7-121351169-T-C		not specified	Uncertain significance (Jan 03, 2024)
7-121360072-T-G		not specified	Uncertain significance (Jan 22, 2024)
7-121360119-G-C		not specified	Uncertain significance (Mar 23, 2022)
7-121364185-T-G		not specified	Uncertain significance (Oct 20, 2021)
7-121378916-G-C		not specified	Uncertain significance (Sep 14, 2023)
7-121382963-C-T		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM3C	protein_coding	protein_coding	ENST00000359943	9	47514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0969	0.896	125725	0	15	125740	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	86	122	0.706	0.00000587	1488
Missense in Polyphen		14	26.062	0.53719		313
Synonymous	1.07	30	38.4	0.780	0.00000185	406
Loss of Function	2.35	4	13.2	0.302	5.56e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000265	0.000265
Ashkenazi Jewish	0.00	0.00
East Asian	0.000125	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000458	0.0000440
Middle Eastern	0.000125	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in retinal laminar formation. Promotes epithelial to mesenchymal transition.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.827
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.335
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.421

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam3c

Gene ontology

• Biological process: platelet degranulation;multicellular organism development;biological_process;regulation of signaling receptor activity;negative regulation of gluconeogenesis
• Cellular component: extracellular region;Golgi apparatus;platelet dense granule lumen;extracellular exosome
• Molecular function: cytokine activity;protein binding