FAM3B

FAM3 metabolism regulating signaling molecule B

Basic information

Region (hg38): 21:41304211-41357727

Previous symbols: [ "C21orf11" ]

Links

ENSG00000183844 ∙ NCBI:54097 ∙ OMIM:608617 ∙ HGNC:1253 ∙ Uniprot:P58499 ∙ 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 FAM3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM3B 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					2	2
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	2	0	3

Variants in FAM3B

This is a list of pathogenic ClinVar variants found in the FAM3B region.

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

Position	Type	Phenotype	Significance	ClinVar
21-41322951-C-T			Benign (Aug 02, 2017)
21-41323026-C-G			Benign (Apr 04, 2018)
21-41323076-G-A			Benign (Aug 02, 2017)
21-41338399-A-G		not specified	Uncertain significance (Mar 20, 2023)
21-41348672-T-C		not specified	Uncertain significance (Apr 19, 2024)
21-41348690-G-T		not specified	Uncertain significance (Apr 18, 2024)
21-41357108-A-T		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM3B	protein_coding	protein_coding	ENST00000357985	8	53220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.43e-8	0.157	125631	0	117	125748	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.461	115	130	0.886	0.00000669	1534
Missense in Polyphen		43	46.297	0.92879		570
Synonymous	-0.517	53	48.4	1.09	0.00000301	434
Loss of Function	0.141	12	12.5	0.957	6.15e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00184	0.00184
Ashkenazi Jewish	0.000694	0.000695
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000306	0.000299
Middle Eastern	0.000109	0.000109
South Asian	0.000327	0.000327
Other	0.000499	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces apoptosis of alpha and beta cells in a dose- and time-dependent manner. {ECO:0000269|PubMed:16114871}.

Recessive Scores

• pRec: 0.0867

Intolerance Scores

• loftool: 0.894
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0589
• hipred: N
• hipred_score: 0.167

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.129

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam3b
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: apoptotic process;regulation of signaling receptor activity;insulin secretion;glucose homeostasis
• Cellular component: extracellular region;extracellular exosome
• Molecular function: cytokine activity