TAFA3

TAFA chemokine like family member 3, the group of TAFA chemokine like family

Basic information

Region (hg38): 1:112718905-112727235

Previous symbols: [ "FAM19A3" ]

Links

ENSG00000184599 ∙ NCBI:284467 ∙ OMIM:617497 ∙ HGNC:21590 ∙ Uniprot:Q7Z5A8 ∙ 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 TAFA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAFA3 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			14	5		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	5	0

Variants in TAFA3

This is a list of pathogenic ClinVar variants found in the TAFA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-112722249-G-A		not specified	Uncertain significance (Jan 19, 2024)
1-112722270-G-A		not specified	Likely benign (Apr 25, 2022)
1-112722286-T-G		not specified	Uncertain significance (Feb 06, 2024)
1-112722295-C-A		not specified	Uncertain significance (Aug 10, 2021)
1-112722336-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-112723022-T-C		not specified	Uncertain significance (Apr 09, 2024)
1-112723024-C-A		not specified	Likely benign (Feb 06, 2024)
1-112723109-C-T		not specified	Uncertain significance (Oct 30, 2023)
1-112723159-G-A		not specified	Uncertain significance (Jan 31, 2024)
1-112723972-G-C		not specified	Uncertain significance (Dec 21, 2022)
1-112723977-G-C		not specified	Uncertain significance (Mar 28, 2024)
1-112724020-C-T		not specified	Likely benign (Dec 05, 2022)
1-112724057-C-G		not specified	Likely benign (May 16, 2024)
1-112724064-G-A		not specified	Uncertain significance (Oct 10, 2023)
1-112724067-A-C		not specified	Likely benign (Feb 05, 2024)
1-112724085-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-112724088-A-G		not specified	Uncertain significance (Mar 29, 2022)
1-112724094-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-112724112-G-A		not specified	Uncertain significance (Feb 21, 2024)
1-112726636-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-112726654-C-T		not specified	Likely benign (Feb 05, 2024)
1-112726661-G-A		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAFA3	protein_coding	protein_coding	ENST00000369630	4	6817

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000367	0.387	125420	0	13	125433	0.0000518

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.131	99	103	0.964	0.00000597	1052
Missense in Polyphen		26	20.077	1.295		234
Synonymous	-0.834	49	42.1	1.16	0.00000225	368
Loss of Function	0.217	7	7.65	0.915	3.27e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000628	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.0000549	0.0000529
Middle Eastern	0.000223	0.000218
South Asian	0.0000329	0.0000327
Other	0.000179	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of microglia polarization. {ECO:0000250|UniProtKB:Q7TPG6}.

Intolerance Scores

• loftool: 0.402
• rvis_EVS: 0.9
• rvis_percentile_EVS: 89.39

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.215

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.122

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam19a3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of microglial cell activation;positive regulation of microglial cell activation
• Cellular component: extracellular space