AKNAD1

AKNA domain containing 1

Basic information

Region (hg38): 1:108815898-108963484

Previous symbols: [ "C1orf62" ]

Links

ENSG00000162641 ∙ NCBI:254268 ∙ ∙ HGNC:28398 ∙ Uniprot:Q5T1N1 ∙ 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 AKNAD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AKNAD1 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			53	6		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	6	0

Variants in AKNAD1

This is a list of pathogenic ClinVar variants found in the AKNAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-108816177-T-G		not specified	Uncertain significance (Mar 25, 2024)
1-108816184-C-T		not specified	Likely benign (Apr 06, 2023)
1-108816226-G-A		not specified	Likely benign (Jun 12, 2023)
1-108817057-T-C		not specified	Uncertain significance (Mar 23, 2022)
1-108817077-A-C		not specified	Uncertain significance (Oct 03, 2022)
1-108817143-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-108820558-G-A		not specified	Uncertain significance (May 07, 2024)
1-108820591-C-T		not specified	Uncertain significance (Sep 29, 2022)
1-108823381-T-C		not specified	Uncertain significance (Dec 02, 2021)
1-108823433-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-108823586-C-A		not specified	Uncertain significance (Mar 25, 2022)
1-108827229-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-108827237-T-C		not specified	Uncertain significance (Jul 06, 2021)
1-108827292-C-A		not specified	Uncertain significance (Jul 19, 2023)
1-108830574-C-A		not specified	Uncertain significance (Oct 18, 2021)
1-108830586-C-G		not specified	Uncertain significance (Aug 22, 2023)
1-108830586-C-T		not specified	Uncertain significance (Apr 26, 2023)
1-108830604-G-A		not specified	Uncertain significance (Dec 11, 2023)
1-108830631-G-A		not specified	Uncertain significance (Jun 23, 2021)
1-108834496-G-A		not specified	Likely benign (Aug 02, 2023)
1-108834526-T-C		not specified	Uncertain significance (May 28, 2024)
1-108834984-G-T		not specified	Uncertain significance (Feb 07, 2023)
1-108835031-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-108835055-A-G		not specified	Uncertain significance (Dec 14, 2023)
1-108837569-A-C		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AKNAD1	protein_coding	protein_coding	ENST00000370001	15	147587

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.62e-23	0.00210	124471	16	1259	125746	0.00508

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0565	430	427	1.01	0.0000204	5512
Missense in Polyphen		62	68.32	0.90749		1039
Synonymous	0.734	147	159	0.926	0.00000862	1534
Loss of Function	0.389	36	38.6	0.932	0.00000179	512

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00182	0.00170
Ashkenazi Jewish	0.000131	0.0000992
East Asian	0.0165	0.0164
Finnish	0.0321	0.0321
European (Non-Finnish)	0.00120	0.00120
Middle Eastern	0.0165	0.0164
South Asian	0.00252	0.00252
Other	0.00521	0.00506

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.984
• rvis_EVS: 0.83
• rvis_percentile_EVS: 88.11

Haploinsufficiency Scores

• pHI: 0.0786
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aknad1