AKNAD1

protein-coding

AKNA domain containing 1

Gene summary

This gene encodes a protein which contains a domain found in an AT-hook-containing transcription factor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

Previous symbols:

C1orf62

MANE transcript

NM_152763.5

Inheritance

—

ClinVar variants

U:111B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr1:108,815,898-108,963,484

External References & Databases

Ensembl (ENSG00000162641)

Transcript & Mutation Effects

hg38 • Region Span ~147.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AKNAD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 122

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152763.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			110 clinvar	15 clinvar		125
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	111	15	0	126

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152763.5	RefSeq	NP_689976.2	15	MANE Select
ENST00000370001.8	Ensembl	ENSP00000359018.3	15	MANE Select
ENST00000357393.6	Ensembl	ENSP00000349968.6	5	Standard
ENST00000369994.5	Ensembl	ENSP00000359011.1	13	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370001
Coding exons: 15
Length: 147587
Individuals with no LoFs: 124471
Homozygous LoFs: 16
Heterozygous LoFs: 1259
Defined: 125746
p: 0.00508

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0565	430	427	1.01	0.0000204	5512
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00062	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00013	0.000099	rare
East Asian	0.016	0.016	notable
Finnish	0.032	0.032	notable
European (Non-Finnish)	0.0012	0.0012	notable
South Asian	0.0025	0.0025	notable
Other	0.0052	0.0051	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.984
RVIS EVS: 0.83
RVIS percentile EVS: 88.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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