CARF

calcium responsive transcription factor

Basic information

Region (hg38): 2:202912214-202988263

Previous symbols: [ "ALS2CR8" ]

Links

ENSG00000138380 ∙ NCBI:79800 ∙ OMIM:607586 ∙ HGNC:14435 ∙ Uniprot:Q8N187 ∙ 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 CARF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CARF 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					2	2
missense			40	7	2	49
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	40	8	5

Variants in CARF

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

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

Position	Type	Phenotype	Significance	ClinVar
2-202941934-A-C		not specified	Uncertain significance (Dec 13, 2021)
2-202941943-A-G		not specified	Uncertain significance (Jan 26, 2022)
2-202942764-G-A		not specified	Uncertain significance (Oct 04, 2024)
2-202942765-A-T		not specified	Uncertain significance (Oct 26, 2022)
2-202942815-C-T		not specified	Uncertain significance (Aug 04, 2023)
2-202942858-C-T		not specified	Uncertain significance (Jan 23, 2024)
2-202942869-A-G		not specified	Uncertain significance (Jan 19, 2025)
2-202942888-A-G		not specified	Uncertain significance (Dec 30, 2024)
2-202942929-T-C		not specified	Uncertain significance (Mar 02, 2023)
2-202942947-G-A		not specified	Uncertain significance (Oct 16, 2024)
2-202952574-C-T			Likely benign (Oct 01, 2024)
2-202952595-C-A		not specified	Uncertain significance (Feb 26, 2024)
2-202952626-T-A		not specified	Uncertain significance (Apr 23, 2024)
2-202952631-C-G		not specified	Uncertain significance (Jul 22, 2022)
2-202952641-T-C		not specified	Uncertain significance (Jun 02, 2024)
2-202952647-A-G		not specified	Uncertain significance (Aug 26, 2024)
2-202952676-C-T		not specified	Uncertain significance (Sep 26, 2023)
2-202954043-A-G		not specified	Uncertain significance (Dec 16, 2022)
2-202954046-G-C		not specified	Uncertain significance (Feb 25, 2025)
2-202954047-T-C			Likely benign (Apr 09, 2018)
2-202954052-G-A		not specified	Uncertain significance (May 27, 2022)
2-202954056-A-G		not specified	Uncertain significance (Feb 26, 2025)
2-202954058-A-G		not specified	Likely benign (May 07, 2024)
2-202954110-C-T		not specified	Uncertain significance (Feb 17, 2024)
2-202954133-G-A		not specified	Likely benign (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CARF	protein_coding	protein_coding	ENST00000402905	14	74850

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.04e-7	0.999	124750	0	43	124793	0.000172

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	311	379	0.820	0.0000184	4735
Missense in Polyphen		79	114.75	0.68846		1497
Synonymous	0.810	116	128	0.909	0.00000579	1393
Loss of Function	2.93	16	34.6	0.463	0.00000147	443

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000775	0.000775
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000972	0.0000971
Middle Eastern	0.0000556	0.0000556
South Asian	0.000141	0.000131
Other	0.000509	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional activator that mediates the calcium- and neuron-selective induction of BDNF exon III transcription. Binds to the consensus calcium-response element CaRE1 5'-CTATTTCGAG-3' sequence. {ECO:0000269|PubMed:11832226, ECO:0000269|PubMed:22174809}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.82

Haploinsufficiency Scores

• pHI: 0.215
• hipred: N
• hipred_score: 0.233
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Carf
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cellular response to potassium ion;positive regulation of transcription from RNA polymerase II promoter in response to calcium ion;cellular response to calcium ion
• Cellular component: nucleus;nucleoplasm;nucleolus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity