ANKEF1

protein-coding

ankyrin repeat and EF-hand domain containing 1, the group of EF-hand domain containing|Ankyrin repeat domain containing

Gene summary

Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ANKRD5

MANE transcript

NM_022096.6

Inheritance

—

ClinVar variants

U:132B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr20:9,986,126-10,058,303

External References & Databases

Ensembl (ENSG00000132623)

Transcript & Mutation Effects

hg38 • Region Span ~72.2 kb

Loading mutation effect viewer...

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 ANKEF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 133

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022096.6. 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			130 clinvar	4 clinvar		134
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	132	4	0	136

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022096.6	RefSeq	NP_071379.3	9	MANE Select
ENST00000378392.6	Ensembl	ENSP00000367644.1	9	MANE Select
NM_001303472.2	RefSeq	NP_001290401.1	7	Standard
NM_198798.3	RefSeq	NP_942093.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

calcium ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378380
Coding exons: 9
Length: 70637
Individuals with no LoFs: 125617
Homozygous LoFs: 0
Heterozygous LoFs: 130
Defined: 125747
p: 0.000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.506	408	438	0.932	0.0000236	5087
Missense (PolyPhen)		155	157.09	0.98667		1825
Synonymous	0.676	153	164	0.933	0.00000961	1509
Loss of Function	1.83	19	29.8	0.638	0.00000165	404

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00049	0.00049	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0030	0.0030	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.00036	0.00036	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0932

Intolerance Scores

RVIS EVS: -0.37
RVIS percentile EVS: 28.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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