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.

• not_specified (34 variants)

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. These statistics are base on transcript: NM_000182759.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	1		2
missense			22	5		27
nonsense				1		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	7	0

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