TCAF1

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

Basic information

Region (hg38): 7:143851375-143902198

Previous symbols: [ "FAM115A" ]

Links

ENSG00000198420 ∙ NCBI:9747 ∙ OMIM:616251 ∙ HGNC:22201 ∙ Uniprot:Q9Y4C2 ∙ 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 TCAF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCAF1 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in TCAF1

This is a list of pathogenic ClinVar variants found in the TCAF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-143857169-A-G		not specified	Uncertain significance (May 22, 2023)
7-143857296-T-C		not specified	Uncertain significance (Aug 19, 2021)
7-143858957-A-C		not specified	Uncertain significance (Jun 11, 2021)
7-143859122-T-A		not specified	Uncertain significance (Mar 28, 2023)
7-143876071-C-G		not specified	Uncertain significance (May 01, 2023)
7-143876103-G-A		not specified	Uncertain significance (Dec 14, 2021)
7-143876185-T-C		not specified	Likely benign (Aug 16, 2022)
7-143876239-C-T		not specified	Uncertain significance (Apr 15, 2024)
7-143876278-C-T		not specified	Uncertain significance (Oct 06, 2022)
7-143876347-G-T		not specified	Uncertain significance (Feb 28, 2024)
7-143876436-C-T		not specified	Uncertain significance (Sep 26, 2023)
7-143876514-A-G		not specified	Uncertain significance (Dec 01, 2022)
7-143876545-C-G		not specified	Uncertain significance (May 27, 2022)
7-143876553-T-C		not specified	Uncertain significance (Oct 05, 2023)
7-143876605-C-A		not specified	Uncertain significance (Oct 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCAF1	protein_coding	protein_coding	ENST00000479870	8	50824

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.618	0.381	123236	0	1	123237	0.00000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	142	189	0.752	0.00000992	5895
Missense in Polyphen		34	65.261	0.52098		1876
Synonymous	0.636	70	77.1	0.908	0.00000446	1900
Loss of Function	2.62	2	11.7	0.172	4.98e-7	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000618
Ashkenazi Jewish	0.00	0.00
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

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

Recessive Scores

• pRec: 0.0896

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.519
• ghis: 0.643

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tcaf1

Gene ontology

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