ATF7IP

protein-coding

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

Gene summary

ATF7IP is a multifunctional nuclear protein that associates with heterochromatin. It can act as a transcriptional coactivator or corepressor depending upon its binding partners (summary by Liu et al., 2009 [PubMed 19106100]).[supplied by OMIM, Nov 2010]

MANE transcript

NM_018179.5

Inheritance

—

ClinVar variants

U:149B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr12:14,365,676-14,502,931

External References & Databases

Ensembl (ENSG00000171681)

Transcript & Mutation Effects

hg38 • Region Span ~137.3 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 ATF7IP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018179.5. 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			1 clinvar	2 clinvar	3 clinvar	6
missense			138 clinvar	11 clinvar	4 clinvar	153
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	149	13	7	169

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018179.5	RefSeq	NP_060649.3	14	MANE Select
ENST00000261168.9	Ensembl	ENSP00000261168.4	14	MANE Select
NM_001286514.2	RefSeq	NP_001273443.1	14	Standard
NM_001286515.2	RefSeq	NP_001273444.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

PKMTs methylate histone lysines
Chromatin modifying enzymes
Chromatin organization

Biological Process

negative regulation of transcription by RNA polymerase II
DNA methylation
viral process
negative regulation of transcription, DNA-templated
positive regulation of transcription, DNA-templated

Molecular Function

transcription corepressor activity
protein binding
ATPase activity

Cellular Component

nucleus
nucleoplasm
transcription factor complex
cytosol
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261168
Coding exons: 14
Length: 133088
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125724
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.78	543	673	0.807	0.0000337	8282
Missense (PolyPhen)		42	60.88	0.68988		836
Synonymous	0.123	238	240	0.990	0.0000121	2615
Loss of Function	5.85	5	49.4	0.101	0.00000299	569

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

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. Required to stimulate histone methyltransferase activity of SETDB1 and facilitate the conversion of dimethylated to trimethylated H3 'Lys-9' (H3K9me3). The complex formed with MBD1 and SETDB1 represses transcription and couples DNA methylation and histone H3 'Lys-9' trimethylation (H3K9me3). Facilitates telomerase TERT and TERC gene expression by SP1 in cancer cells. {ECO:0000269|PubMed:12665582, ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:19106100}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.155
RVIS EVS: 0.47
RVIS percentile EVS: 78.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.613

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High