ATF7IP2

protein-coding

activating transcription factor 7 interacting protein 2, the group of Fibronectin type III domain containing

Gene summary

Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001393719.1

Inheritance

—

ClinVar variants

U:106B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr16:10,326,434-10,483,638

External References & Databases

Ensembl (ENSG00000166669)

Transcript & Mutation Effects

hg38 • Region Span ~157.2 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 ATF7IP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 112

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001393719.1. 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				1 clinvar		1
missense			102 clinvar	13 clinvar		115
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	106	14	0	120

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 55 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001393719.1	RefSeq	NP_001380648.1	10	MANE Select
ENST00000562102.6	Ensembl	ENSP00000457731.2	10	MANE Select
NM_001256160.3	RefSeq	NP_001243089.1	9	Standard
NM_001352120.2	RefSeq	NP_001339049.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396560
Coding exons: 10
Length: 157205
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125728
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.32	409	341	1.20	0.0000163	4496
Missense (PolyPhen)		84	76.092	1.1039		1094
Synonymous	-1.52	143	122	1.18	0.00000595	1256
Loss of Function	3.67	7	27.9	0.251	0.00000135	401

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000096	0.000092	rare
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0.000078	0.000065	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Recruiter that couples transcriptional factors to general transcription apparatus and thereby modulates transcription regulation and chromatin formation. Can both act as an activator or a repressor depending on the context. Mediates MBD1-dependent transcriptional repression, probably by recruiting complexes containing SETDB1. The complex formed with MBD1 and SETDB1 represses transcription and probably couples DNA methylation and histone H3 'Lys-9' trimethylation (H3K9me3) activity (Probable). {ECO:0000305}.;

Recessive Scores

pRec: 0.0843

Intolerance Scores

LoFtool: 0.604
RVIS EVS: 0.07
RVIS percentile EVS: 59.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.710

Gene Damage Prediction

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