CT47B1

cancer/testis antigen family 47 member B1, the group of CT antigen family 47

Basic information

Region (hg38): X:120872607-120875866

Links

ENSG00000236446 ∙ NCBI:643311 ∙ OMIM:300790 ∙ HGNC:33293 ∙ Uniprot:P0C2W7 ∙ 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 CT47B1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CT47B1 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			64	6		70
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	8	0

Variants in CT47B1

This is a list of pathogenic ClinVar variants found in the CT47B1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-120873904-C-T		not specified	Conflicting classifications of pathogenicity (Mar 01, 2023)
X-120873909-G-T		not specified	Uncertain significance (Sep 04, 2024)
X-120873930-A-G		not specified	Likely benign (Apr 28, 2022)
X-120873935-C-G		not specified	Uncertain significance (Oct 12, 2024)
X-120874000-C-T			Likely benign (Mar 01, 2023)
X-120874910-G-A		not specified	Uncertain significance (Dec 03, 2021)
X-120874935-C-A		not specified	Uncertain significance (Feb 28, 2023)
X-120874938-C-A		not specified	Uncertain significance (Mar 07, 2024)
X-120874950-T-C		not specified	Uncertain significance (May 10, 2024)
X-120874974-C-G		not specified	Uncertain significance (Jun 17, 2024)
X-120874977-C-A		not specified	Uncertain significance (Jun 17, 2024)
X-120874977-C-T		not specified	Uncertain significance (Nov 24, 2024)
X-120874992-G-T		not specified	Uncertain significance (Feb 26, 2024)
X-120875015-G-A		not specified	Uncertain significance (Sep 14, 2022)
X-120875042-T-G		not specified	Uncertain significance (Sep 02, 2024)
X-120875048-G-A		not specified	Uncertain significance (Feb 27, 2025)
X-120875052-C-A		not specified	Uncertain significance (Apr 13, 2022)
X-120875061-C-G		not specified	Uncertain significance (Feb 19, 2025)
X-120875073-C-T		not specified	Uncertain significance (Jan 21, 2025)
X-120875076-C-A		not specified	Uncertain significance (Jun 14, 2023)
X-120875094-C-A		not specified	Uncertain significance (Jan 17, 2025)
X-120875109-C-G		not specified	Uncertain significance (Sep 03, 2024)
X-120875109-C-T		not specified	Uncertain significance (Aug 10, 2021)
X-120875155-G-T			Likely benign (May 01, 2022)
X-120875188-G-T		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CT47B1	protein_coding	protein_coding	ENST00000371311	2	3323

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.63e-9	0.0226	125367	6	15	125388	0.0000837

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-6.06	347	143	2.43	0.0000138	1921
Missense in Polyphen		93	44.176	2.1052		582
Synonymous	-5.62	137	75.1	1.82	0.00000847	634
Loss of Function	-1.62	10	5.80	1.73	4.05e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000147	0.000147
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000735	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000189	0.000132
Middle Eastern	0.0000735	0.0000544
South Asian	0.0000529	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0456

Gene Damage Prediction

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