C21orf62

chromosome 21 open reading frame 62

Basic information

Region (hg38): 21:32790672-32813743

Previous symbols: [ "C21orf120" ]

Links

ENSG00000205929 ∙ NCBI:56245 ∙ ∙ HGNC:1305 ∙ Uniprot:Q9NYP8 ∙ 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 C21orf62 gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C21orf62 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in C21orf62

This is a list of pathogenic ClinVar variants found in the C21orf62 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-32793980-T-C		not specified	Uncertain significance (Jul 09, 2021)
21-32794046-G-T		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C21orf62	protein_coding	protein_coding	ENST00000536776	1	23069

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00262	0.575	124772	0	23	124795	0.0000922

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.590	105	123	0.851	0.00000666	1463
Missense in Polyphen		34	39.08	0.87001		475
Synonymous	1.20	38	48.7	0.780	0.00000276	425
Loss of Function	0.330	4	4.78	0.837	2.86e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000332	0.000332
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.0000354	0.0000353
Middle Eastern	0.0000556	0.0000556
South Asian	0.000196	0.000196
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.245
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.0539
• 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: 4932438H23Rik

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function