ENKD1

enkurin domain containing 1

Basic information

Region (hg38): 16:67662945-67667265

Previous symbols: [ "C16orf48" ]

Links

ENSG00000124074 ∙ NCBI:84080 ∙ ∙ HGNC:25246 ∙ Uniprot:Q9H0I2 ∙ 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 ENKD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENKD1 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
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in ENKD1

This is a list of pathogenic ClinVar variants found in the ENKD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67663268-G-T		not specified	Uncertain significance (Jul 05, 2023)
16-67663295-C-T		not specified	Uncertain significance (Feb 23, 2023)
16-67663467-C-T		not specified	Uncertain significance (Jan 10, 2023)
16-67663470-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-67663470-G-T		not specified	Uncertain significance (Aug 16, 2021)
16-67663497-G-A		not specified	Uncertain significance (Sep 20, 2023)
16-67663512-C-A		not specified	Uncertain significance (Mar 14, 2023)
16-67663512-C-T		not specified	Uncertain significance (Oct 03, 2024)
16-67663528-G-A		not specified	Uncertain significance (Aug 19, 2024)
16-67663546-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-67663681-G-A		not specified	Uncertain significance (Nov 27, 2023)
16-67663691-A-C		not specified	Uncertain significance (Aug 12, 2021)
16-67663693-T-A		not specified	Uncertain significance (May 16, 2023)
16-67663724-C-T		not specified	Uncertain significance (Oct 04, 2024)
16-67663786-T-C		not specified	Uncertain significance (Aug 04, 2021)
16-67663792-C-T		not specified	Uncertain significance (Feb 06, 2023)
16-67663946-G-A			Likely benign (Jan 01, 2023)
16-67663986-G-A		not specified	Uncertain significance (Sep 09, 2024)
16-67663995-C-T		not specified	Uncertain significance (Apr 05, 2023)
16-67664026-A-G		not specified	Uncertain significance (Mar 29, 2023)
16-67664052-G-T		not specified	Uncertain significance (Oct 16, 2024)
16-67665025-C-T		not specified	Uncertain significance (Nov 11, 2024)
16-67665039-G-C		not specified	Uncertain significance (Apr 29, 2024)
16-67665046-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-67665071-C-A		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENKD1	protein_coding	protein_coding	ENST00000243878	7	4321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.53e-8	0.288	125614	1	121	125736	0.000485

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.230	224	215	1.04	0.0000132	2173
Missense in Polyphen		54	54.993	0.98193		615
Synonymous	0.594	79	86.0	0.918	0.00000430	751
Loss of Function	0.573	13	15.4	0.843	7.21e-7	174

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000204	0.000204
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000221	0.000217
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000444	0.000422
Middle Eastern	0.000221	0.000217
South Asian	0.00194	0.00190
Other	0.000507	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0987

Intolerance Scores

• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.17

Haploinsufficiency Scores

• pHI: 0.257
• hipred: N
• hipred_score: 0.216
• ghis: 0.430

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: Enkd1

Gene ontology

• Cellular component: cytoplasmic microtubule;microtubule cytoskeleton
• Molecular function: protein binding