EVA1C

eva-1 homolog C

Basic information

Region (hg38): 21:32412006-32515397

Previous symbols: [ "C21orf64", "C21orf63", "FAM176C" ]

Links

ENSG00000166979 ∙ NCBI:59271 ∙ ∙ HGNC:13239 ∙ Uniprot:P58658 ∙ 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 EVA1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EVA1C 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				1	1	2
missense			27	1	2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	27	2	3

Variants in EVA1C

This is a list of pathogenic ClinVar variants found in the EVA1C region.

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

Position	Type	Phenotype	Significance	ClinVar
21-32412896-C-T		not specified	Uncertain significance (Jan 16, 2024)
21-32412899-G-A		not specified	Uncertain significance (Dec 21, 2022)
21-32412917-C-T		not specified	Uncertain significance (Oct 27, 2023)
21-32412920-C-A			Likely benign (Jun 22, 2023)
21-32412927-T-C		not specified	Uncertain significance (Sep 14, 2023)
21-32412977-T-G		not specified	Uncertain significance (Feb 02, 2022)
21-32412984-A-T		not specified	Uncertain significance (Jan 08, 2024)
21-32453359-G-C		not specified	Uncertain significance (Apr 18, 2023)
21-32453378-A-G		not specified	Uncertain significance (Aug 09, 2021)
21-32453386-C-T		not specified	Uncertain significance (Jan 26, 2023)
21-32453407-C-G		not specified	Uncertain significance (Jul 14, 2021)
21-32457648-A-T		not specified	Uncertain significance (Feb 27, 2024)
21-32457651-C-T		not specified	Uncertain significance (Apr 27, 2022)
21-32457652-G-A		not specified	Uncertain significance (Nov 08, 2022)
21-32467740-C-G		not specified	Uncertain significance (Mar 16, 2022)
21-32467744-A-G		not specified	Uncertain significance (Apr 26, 2024)
21-32467842-C-A		not specified	Uncertain significance (Oct 26, 2021)
21-32467842-C-G		not specified	Uncertain significance (Jul 20, 2021)
21-32467843-C-G		not specified	Uncertain significance (Mar 16, 2022)
21-32495163-C-T			Benign (Jul 16, 2018)
21-32495164-G-T		not specified	Uncertain significance (Aug 13, 2021)
21-32501436-C-T		not specified	Uncertain significance (Sep 14, 2022)
21-32503926-G-A		not specified	Uncertain significance (May 24, 2024)
21-32503934-T-G		not specified	Uncertain significance (Jul 08, 2022)
21-32504009-A-G		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EVA1C	protein_coding	protein_coding	ENST00000300255	8	103394

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00146	0.992	125726	0	20	125746	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.802	204	239	0.854	0.0000127	2851
Missense in Polyphen		57	86.606	0.65815		1033
Synonymous	0.644	91	99.2	0.918	0.00000562	856
Loss of Function	2.40	8	19.4	0.413	9.03e-7	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000341	0.000336
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds heparin. {ECO:0000269|PubMed:19470522}.

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.575
• ghis: 0.517

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: Eva1c
• Phenotype: vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular region;integral component of membrane
• Molecular function: heparin binding;carbohydrate binding