TAFA2

TAFA chemokine like family member 2, the group of TAFA chemokine like family

Basic information

Region (hg38): 12:61708272-62279150

Previous symbols: [ "FAM19A2" ]

Links

ENSG00000198673 ∙ NCBI:338811 ∙ OMIM:617496 ∙ HGNC:21589 ∙ Uniprot:Q8N3H0 ∙ 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 TAFA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAFA2 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			4			4
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	5	0	0

Variants in TAFA2

This is a list of pathogenic ClinVar variants found in the TAFA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-61753671-T-C		not specified	Uncertain significance (Dec 01, 2022)
12-61754957-T-C		not specified	Uncertain significance (Jan 31, 2022)
12-61867337-C-A		not specified	Uncertain significance (Jan 26, 2022)
12-61867374-T-G		not specified	Uncertain significance (Jan 06, 2023)
12-61867415-C-T		not specified	Uncertain significance (Feb 14, 2023)
12-61875935-ATATAGAATAAGAAAGGAAAATTCCAATTATATGTAGCCTTTTATAGATGGCTAAATCATAAGCCTTATATTTAATTTTGTGATTATATATGGTAAAAAGAGAGATAGCTCTGCACATAATATCTAATTCTGTATATAATATTCATAATAAAACATTTTCTTTCTTTTTTAATAAGACTTTTATAATGCAAATAATAAGGCTTTTATCAATGCAAATAAGCTATGGTAATGGAACCAGTTCTAAATATTTCTTCAGTCTATTATCATTGGGACTAGTTAAGACTTTCATTCCTTTAGTTCTGGTGTACCTGTTCTCTTGGGAAATGAGGCACAGAAGAAATCCACTTCACCTCAGCTCTTTCTCCTGCATGCTGGCAAAGGAGTGAAAAAGTGAGTGAGAACAACGAAAACAATCTTTAAGAGTTCTTTGTTAGGATAAAGTTTGTGGTCCAAGAACATTTATTCTCACCATAGTAACACCTACATATATGAAGGATTCTCCATTTTATGCATTTAACCATCCAGTATGGTCAATATGCCAGCCAGCACTAGCTAGTTAACAGCACGCATTCAAGAGAGCAAAACAGCTTAACCAGCAAACCATTAAAACATGGAACCTCCTCCTCAACACAGATTGTTCTCAAAGGTAGGTGAACTGAAGAGCTAAAGTTGCATATCCGAAGGCCTCTGCTCATATAACCATCCCTTCTAAAGCACCAACATCAACATATTTCAACCATACCATCAAAAATTACAAAAGCAAACAAACCATTAAAAAAAAAAGATAGTAGTTATGTGTCAAAAAGAATGCTATTCTATGTTCTCAAAAGAAGCCAAAAGAAAAGAGTCCAAGAATAGACTGTTTAATCAACTTCACTTGAATTCACACTTCTCTCTGAGAATAATAGTTTAAGCAAAATTTTTGGACAATTATGTGCACTAGCGTTAAATCCCTGAGCACAGCAACGTCACAATGAAAGAGACAGCGATGCTGGGACCCACACACTTTTATAACTACATTCTATTCACACTCCTTATATGTGTTTGATAGTTGTACATTACTTCATATACTTTAACGAGCTGTCTTTGAGGGAAAGGTAGAACATTACCAGATTTTAATATAACAAAGTACCATACTCAGCTTTCAGCTAACAGCTTAAGCAACTGAGAACTCAACTGATTAAGAATCAAAGCAGCAACCACTCTGTGCTACAAACCTCAGTCTACAGTAAGCCTCTATAACATATTGCTTTCTGACTTGCTCTTTTTGCAATAAGATTTCAGTAGCTTTTAGAATCTCACTTTTTTACTCTTTCCCTTTATGAATAAAATTGGTCACATAATACACACTACTCTAACTTCTATTTGCCATCAGCCGCTTTGTTCCACCCCTAACATTTTCCTTATGGATGAATTTGGTTTCCTCAGTCATGATGCAGGTATTTTCCTGCAGTATGCAATCATATGGCAAAGCAGCAGTCAAGTGGTTAAATGTGCAATCGTGAGAAATTTTCCCACTGGTGAGATGTATTCTATTGTGAAATTATGCCCCAAGGTGGTGGTGGAAGCCTATTACCTGGGTCTATTTTCAAAAAATTCTCCAAAGAACACCCTGAGGAAAGCCCTACATTATGGGGATATGAAGAACTAGTCCAAACTACAGCCATCGTCATTTCATATTGGCTTAAAACCTACTGACCTTATTTCTTCTCAATTTGTATCCCATTACTTCAATTGCTAGGAAGAAGGATTCAGGACACATCAGATATAATACTACACAAAACAAGTACCAGATATCACTACAGTTTAGCAAGAATTTAACCAGTAATCCCTGAGTTAACACTCTTCTTGCAATGTACAATGGACATGAGAGTACTCTGTAAACTGTATAGTAGTGTATAAATTAGACTTATTACCAAATCATACTAAATTAGGTAATAGGGTGAATGGATAAACAAATTGTGATTTTTATATATATATATATATATATACACACACACACACACATACATATACATATATATACACACACAGTGGAATATTATTCAGCCTTAAAAAGAAATTACAACATAGATGAATTTGGAAACATGTTAAGTGAAATAAGCCAGACACAAAAGTACAAATACTGTGTGGTCCTACTTACATGAGAGATACCTAGAATAGTCAAATTCGTTGAGACAGAAAGTAGAATAGAGATTACCAGGAGCTGAAGGGAGGGAGAAATAGAGAGTTACTATTTAATGAATATGGAGTTTTTGTACAGGATGACTTTTAAAAGAGTTCTGGAATAGATAAGTGGTAATGTACAACATTGTGAATGTACTTAATGCTGCTGAATTGTACAAAAAATGGCTACAATGGTAAACTTTATGTTATGTCTATTTTACAACAATAAAAATGAAGAAAAACAGATAAAATGGCAAGAGTCGTAATGGGAACAGCTCTGCTCATTGGCTCTACCATATAACCTACATTTATTTTCTTCGTGGCACTGAACAGTATTTGAAATAGTATTAACCTATTTGCTTACTTGTTTATTGTCTCTCTCTTCCCCTACTAGAATACAATCTACTATAAGAGCACAAACCTATGCCTTCTATTTCACTACTTTATTTCCAGCATTTATGTTTCTTATCACAGAGTGTGTGCAGAATAAATATTTGTTGAATAAATAAATAGATGGAAGAAACACTACATATGTCCTTTTAATTTTGAGCTTGGTTGCTCTGCATGATCACACACATTTTCTTATGCCCAATAACATTTAATGTCTCTACCTCTTGTAGGCAGTAGAATACTTTCAATTGTTGTTTATATTATATGTAAGTCTTGTATCTGTAAATAGAAGCTAAGC-A		Normal pregnancy	not provided (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAFA2	protein_coding	protein_coding	ENST00000416284	4	570892

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.341	0.646	125315	0	2	125317	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	48	72.3	0.664	0.00000367	847
Missense in Polyphen		15	36.761	0.40804		419
Synonymous	0.721	21	25.6	0.819	0.00000136	244
Loss of Function	2.10	2	8.66	0.231	4.51e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.0000998	0.0000994
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

Recessive Scores

• pRec: 0.0993

Intolerance Scores

• loftool: 0.216
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• pHI: 0.485
• hipred: Y
• hipred_score: 0.502
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam19a2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Cellular component: cytoplasm