CYYR1

cysteine and tyrosine rich 1

Basic information

Region (hg38): 21:26466208-26573286

Previous symbols: [ "C21orf95" ]

Links

ENSG00000166265 ∙ NCBI:116159 ∙ OMIM:616020 ∙ HGNC:16274 ∙ Uniprot:Q96J86 ∙ 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 CYYR1 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYYR1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in CYYR1

This is a list of pathogenic ClinVar variants found in the CYYR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-26468530-G-T		not specified	Uncertain significance (Feb 27, 2023)
21-26468593-A-T		not specified	Uncertain significance (Apr 27, 2023)
21-26468601-A-G		not specified	Uncertain significance (Feb 12, 2024)
21-26480349-A-G		not specified	Uncertain significance (Nov 08, 2022)
21-26572919-C-A		not specified	Uncertain significance (Jan 18, 2023)
21-26572930-G-T		not specified	Uncertain significance (Mar 08, 2024)
21-26572931-G-A		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CYYR1	protein_coding	protein_coding	ENST00000299340	4	107076

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000444	0.437	125435	0	311	125746	0.00124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.492	111	97.3	1.14	0.00000537	987
Missense in Polyphen		58	46.668	1.2428		476
Synonymous	0.298	37	39.4	0.940	0.00000269	312
Loss of Function	0.0689	5	5.17	0.967	2.18e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00121
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000555	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00193	0.00192
Middle Eastern	0.0000555	0.0000544
South Asian	0.00187	0.00186
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0929

Intolerance Scores

• loftool: 0.611
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.08

Haploinsufficiency Scores

• pHI: 0.232
• hipred: N
• hipred_score: 0.231
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0578

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cyyr1

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of membrane
• Molecular function: molecular_function