TEX56P

testis expressed 56, pseudogene

Basic information

Region (hg38): 6:4087534-4122032

Previous symbols: [ "C6orf201" ]

Links

ENSG00000185689 ∙ NCBI:404220 ∙ ∙ HGNC:21620 ∙ ∙ ∙ 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 TEX56P gene.

• Inborn genetic diseases (15 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEX56P 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15		2	17
Total	0	0	15	0	2

Variants in TEX56P

This is a list of pathogenic ClinVar variants found in the TEX56P region.

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

Position	Type	Phenotype	Significance	ClinVar
6-4099018-C-G		not specified	Uncertain significance (Aug 17, 2021)
6-4099122-G-A		not specified	Uncertain significance (Jul 16, 2021)
6-4115909-C-T		not specified	Uncertain significance (Dec 12, 2023)
6-4117312-G-T		not specified	Uncertain significance (Feb 13, 2024)
6-4117360-A-G		not specified	Uncertain significance (Sep 25, 2023)
6-4117373-G-A			Benign (Aug 15, 2017)
6-4117414-G-T		not specified	Uncertain significance (May 29, 2024)
6-4117442-T-C		not specified	Uncertain significance (May 26, 2024)
6-4119187-T-G		not specified	Uncertain significance (Mar 24, 2023)
6-4119205-T-C		not specified	Uncertain significance (Mar 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEX56P	protein_coding	protein_coding	ENST00000380175	4	51746

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00644	0.762	124766	0	28	124794	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.285	66	72.8	0.906	0.00000386	898
Missense in Polyphen		26	25.678	1.0125		338
Synonymous	0.410	27	29.8	0.905	0.00000186	262
Loss of Function	0.886	4	6.42	0.623	2.67e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000203	0.000203
Middle Eastern	0.000111	0.000111
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Mesodermal Commitment Pathway (Consensus)

Intolerance Scores

• loftool: 0.772
• rvis_EVS: 1.41
• rvis_percentile_EVS: 94.84

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: 4933417A18Rik
• Phenotype: normal phenotype