ANKFN1

protein-coding

ankyrin repeat and fibronectin type III domain containing 1, the group of Ankyrin repeat domain containing|Fibronectin type III domain containing

Gene summary

Predicted to be involved in establishment of mitotic spindle orientation and regulation of establishment of bipolar cell polarity. Predicted to act upstream of or within behavioral fear response; equilibrioception; and locomotor rhythm. Predicted to be active in spindle. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001370326.1

Inheritance

—

ClinVar variants

U:95B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr17:55,882,301-56,517,016

External References & Databases

Ensembl (ENSG00000153930)

Transcript & Mutation Effects

hg38 • Region Span ~634.7 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 ANKFN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370326.1. 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			94 clinvar	2 clinvar		96
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	95	2	0	97

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370326.1	RefSeq	NP_001357255.1	20	MANE Select
ENST00000682825.1	Ensembl	ENSP00000507365.1	20	MANE Select
NM_001365758.1	RefSeq	NP_001352687.1	17	Standard
NM_153228.3	RefSeq	NP_694960.2	17	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000318698
Coding exons: 17
Length: 400702
Individuals with no LoFs: 125658
Homozygous LoFs: 0
Heterozygous LoFs: 90
Defined: 125748
p: 0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.559	383	415	0.923	0.0000215	5023
Missense (PolyPhen)		95	108.46	0.8759		1271
Synonymous	0.196	149	152	0.980	0.00000821	1426
Loss of Function	2.87	23	43.4	0.530	0.00000217	490

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00044	0.00044	rare
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.00047	0.00047	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.793
RVIS EVS: 0.6
RVIS percentile EVS: 82.83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0933

Gene Damage Prediction

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