ANKS1A

protein-coding

ankyrin repeat and sterile alpha motif domain containing 1A, the group of Ankyrin repeat domain containing|Sterile alpha motif domain containing

Gene summary

Predicted to enable ephrin receptor binding activity. Predicted to be involved in ephrin receptor signaling pathway; neuron remodeling; and substrate-dependent cell migration. Predicted to be located in neuron projection. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ANKS1

MANE transcript

NM_015245.3

Inheritance

—

ClinVar variants

U:167B:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr6:34,889,255-35,091,406

External References & Databases

Ensembl (ENSG00000064999)

Transcript & Mutation Effects

hg38 • Region Span ~202.2 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 ANKS1A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 164

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015245.3. 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			3 clinvar	6 clinvar	3 clinvar	12
missense			156 clinvar	8 clinvar	2 clinvar	166
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	167	14	5	186

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015245.3	RefSeq	NP_056060.2	24	MANE Select
ENST00000360359.5	Ensembl	ENSP00000353518.3	24	MANE Select
ENST00000649117.1	Ensembl	ENSP00000497393.1	25	Standard
ENST00000649117.2	Ensembl	ENSP00000497393.1	25	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

EGFR1

Biological Process

substrate-dependent cell migration
neuron remodeling
ephrin receptor signaling pathway
regulation of ephrin receptor signaling pathway

Molecular Function

protein binding
ephrin receptor binding

Cellular Component

nucleoplasm
cytosol
neuron projection

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360359
Coding exons: 24
Length: 202138
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125748
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.81	452	655	0.691	0.0000396	7370
Missense (PolyPhen)		125	246.68	0.50674		2792
Synonymous	0.858	259	277	0.934	0.0000183	2288
Loss of Function	5.42	11	53.9	0.204	0.00000272	628

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.000056	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulator of different signaling pathways. Regulates EPHA8 receptor tyrosine kinase signaling to control cell migration and neurite retraction (By similarity). {ECO:0000250, ECO:0000269|PubMed:17875921}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.396
RVIS EVS: -1.25
RVIS percentile EVS: 5.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.987

Gene Damage Prediction

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