TAFA5

TAFA chemokine like family member 5, the group of TAFA chemokine like family

Basic information

Region (hg38): 22:48489552-48850912

Previous symbols: [ "FAM19A5" ]

Links

ENSG00000219438 ∙ NCBI:25817 ∙ OMIM:617499 ∙ HGNC:21592 ∙ Uniprot:Q7Z5A7 ∙ 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 TAFA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAFA5 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					1	1
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in TAFA5

This is a list of pathogenic ClinVar variants found in the TAFA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-48646639-G-A		not specified	Uncertain significance (Jun 06, 2023)
22-48646664-G-A			Benign (Feb 27, 2018)
22-48646668-G-A		not specified	Uncertain significance (Jun 22, 2023)
22-48646671-C-T		not specified	Uncertain significance (Mar 25, 2022)
22-48646672-G-A		not specified	Uncertain significance (Apr 23, 2024)
22-48646695-A-G		not specified	Uncertain significance (Aug 21, 2023)
22-48646720-C-T		not specified	Uncertain significance (Jun 03, 2022)
22-48646729-G-A		not specified	Uncertain significance (Mar 25, 2024)
22-48707795-G-C		not specified	Uncertain significance (Dec 02, 2022)
22-48707816-A-G		not specified	Uncertain significance (Jan 30, 2024)
22-48707821-G-A		not specified	Uncertain significance (Nov 15, 2021)
22-48707821-G-T		not specified	Uncertain significance (Dec 13, 2023)
22-48707824-G-A		not specified	Uncertain significance (Feb 12, 2024)
22-48707828-G-C		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAFA5	protein_coding	protein_coding	ENST00000402357	4	361453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.447	0.527	122250	0	1	122251	0.00000409

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	49	89.7	0.546	0.00000632	830
Missense in Polyphen		22	50.993	0.43144		397
Synonymous	-1.19	46	36.8	1.25	0.00000279	258
Loss of Function	1.78	1	5.52	0.181	2.33e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000101	0.000101
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

Intolerance Scores

• loftool: 0.0610
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.445
• ghis: 0.420

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: Fam19a5

Gene ontology

• Biological process: regulation of signaling receptor activity
• Cellular component: extracellular space
• Molecular function: cytokine activity