TAFA4

TAFA chemokine like family member 4, the group of TAFA chemokine like family

Basic information

Region (hg38): 3:68731766-68953297

Previous symbols: [ "FAM19A4" ]

Links

ENSG00000163377 ∙ NCBI:151647 ∙ OMIM:617498 ∙ HGNC:21591 ∙ Uniprot:Q96LR4 ∙ 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 TAFA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAFA4 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	1

Variants in TAFA4

This is a list of pathogenic ClinVar variants found in the TAFA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-68733146-C-T		not specified	Uncertain significance (Jul 14, 2023)
3-68733148-C-T			Benign (Jun 26, 2018)
3-68733149-G-A		not specified	Uncertain significance (Mar 19, 2024)
3-68739085-T-C		not specified	Uncertain significance (Oct 26, 2022)
3-68739160-G-A		not specified	Uncertain significance (May 14, 2024)
3-68739174-C-G		not specified	Uncertain significance (Mar 16, 2022)
3-68752887-G-A		not specified	Uncertain significance (Mar 04, 2024)
3-68752908-C-T		not specified	Uncertain significance (May 11, 2022)
3-68752910-G-A		not specified	Uncertain significance (Jan 24, 2024)
3-68752911-G-C		not specified	Uncertain significance (Mar 16, 2022)
3-68752940-C-T		not specified	Uncertain significance (Sep 12, 2023)
3-68752941-G-A		not specified	Uncertain significance (Mar 18, 2024)
3-68752952-C-A		not specified	Uncertain significance (Apr 12, 2024)
3-68752952-C-T		not specified	Uncertain significance (Dec 02, 2022)
3-68752959-T-C		not specified	Uncertain significance (Jun 21, 2021)
3-68752986-C-A		not specified	Uncertain significance (Mar 23, 2023)
3-68752991-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-68880735-T-A		not specified	Uncertain significance (Oct 26, 2021)
3-68880736-G-A		not specified	Uncertain significance (Aug 10, 2021)
3-68880763-A-T		not specified	Uncertain significance (Aug 12, 2021)
3-68880790-C-T		not specified	Uncertain significance (Jul 25, 2023)
3-68880838-C-T		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAFA4	protein_coding	protein_coding	ENST00000295569	5	200845

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000660	0.755	125699	0	4	125703	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.111	91	88.1	1.03	0.00000548	905
Missense in Polyphen		46	43.861	1.0488		443
Synonymous	-0.972	42	34.7	1.21	0.00000231	257
Loss of Function	0.971	6	9.18	0.654	3.89e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0924

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.0982
• hipred: N
• hipred_score: 0.488
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam19a4

Gene ontology

• Biological process: regulation of membrane potential;regulation of sensory perception of pain
• Cellular component: extracellular region
• Molecular function: protein binding