TCAF2

TRPM8 channel associated factor 2, the group of Glutamine amidotransferase class 1 domain containing

Basic information

Region (hg38): 7:143620952-143730410

Previous symbols: [ "FAM139A", "FAM115C" ]

Links

ENSG00000170379

∙ NCBI:285966 ∙ OMIM:616252 ∙ HGNC:26878 ∙ Uniprot:A6NFQ2 ∙ 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 TCAF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCAF2 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 clinvar		1
missense			29 clinvar	1 clinvar		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in TCAF2

This is a list of pathogenic ClinVar variants found in the TCAF2 region.

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

Position	Phenotype	Significance	ClinVar
7-143703169-C-T	not specified	Uncertain significance (Sep 12, 2023)	2587980
7-143703230-T-C	not specified	Uncertain significance (Aug 02, 2021)	2241021
7-143703307-A-T	not specified	Uncertain significance (Oct 03, 2022)	3175020
7-143703350-C-G	not specified	Uncertain significance (Nov 29, 2021)	2262312
7-143703389-A-G	not specified	Uncertain significance (Apr 04, 2024)	3324903
7-143703403-G-A	not specified	Uncertain significance (Apr 18, 2023)	2537857
7-143719683-G-A	not specified	Likely benign (May 30, 2024)	3324902
7-143719762-C-G	not specified	Uncertain significance (Feb 01, 2023)	2473821
7-143719792-G-A	not specified	Uncertain significance (Feb 11, 2022)	2277408
7-143719808-T-C	not specified	Uncertain significance (May 18, 2023)	2517503
7-143719823-A-G	not specified	Uncertain significance (Oct 12, 2021)	2254896
7-143719898-C-T	not specified	Uncertain significance (Nov 14, 2023)	3175021
7-143719925-C-T	not specified	Uncertain significance (Oct 21, 2021)	2380835
7-143719931-G-A	not specified	Uncertain significance (May 13, 2024)	3324905
7-143719955-G-A	not specified	Uncertain significance (Aug 16, 2021)	2376846
7-143719955-G-T	not specified	Uncertain significance (Nov 14, 2023)	3175022
7-143720003-C-T	not specified	Uncertain significance (Mar 02, 2023)	2464111
7-143720031-G-C	not specified	Uncertain significance (May 15, 2024)	3324901
7-143720120-G-T	not specified	Uncertain significance (Sep 13, 2023)	2623117
7-143720177-A-G	not specified	Likely benign (Feb 28, 2023)	2490905
7-143720207-T-C	not specified	Uncertain significance (Jan 05, 2022)	2270535
7-143720232-C-A	not specified	Uncertain significance (Jan 11, 2023)	2471645
7-143720269-G-A	not specified	Uncertain significance (Aug 16, 2021)	2356940
7-143720276-C-T	not specified	Uncertain significance (Aug 08, 2022)	2221164
7-143720291-G-A	not specified	Uncertain significance (Feb 24, 2022)	2367454

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCAF2	protein_coding	protein_coding	ENST00000444908	6	109460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.08e-8	0.0406	125559	1	18	125578	0.0000757

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.499	133	150	0.885	0.00000768	5360
Missense in Polyphen		54	62.939	0.85798		2175
Synonymous	1.70	48	65.5	0.733	0.00000363	1767
Loss of Function	-1.09	10	6.91	1.45	3.50e-7	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000998	0.0000970
Middle Eastern	0.00	0.00
South Asian	0.000229	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Isoform 2: Negatively regulates the plasma membrane cation channel TRPM8 activity. Involved in the recruitment of TRPM8 to the cell surface. Promotes prostate cancer cell migration stimulation in a TRPM8-dependent manner. {ECO:0000269|PubMed:25559186}.;

Haploinsufficiency Scores

pHI: 0.102
hipred
hipred_score
ghis: 0.444

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name: Tcaf2
Phenotype

Gene ontology

Biological process: negative regulation of anion channel activity;positive regulation of cell migration;positive regulation of protein targeting to membrane
Cellular component: plasma membrane;cell junction
Molecular function: ion channel binding