ATF7IP

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

Basic information

Region (hg38): 12:14365675-14502931

Links

ENSG00000171681 ∙ NCBI:55729 ∙ OMIM:613644 ∙ HGNC:20092 ∙ Uniprot:Q6VMQ6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATF7IP gene.

• Inborn genetic diseases (37 variants)
• not provided (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATF7IP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	3	4
missense			34	7	5	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	8	8

Variants in ATF7IP

This is a list of pathogenic ClinVar variants found in the ATF7IP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-14424018-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-14424047-A-C		not specified	Uncertain significance (Feb 15, 2023)
12-14424156-C-T		not specified	Likely benign (Oct 26, 2021)
12-14424259-A-G		not specified	Uncertain significance (May 27, 2022)
12-14424271-C-G		not specified	Uncertain significance (Mar 22, 2023)
12-14424300-C-G		not specified	Uncertain significance (Dec 21, 2021)
12-14424331-T-G			Likely benign (Dec 31, 2019)
12-14424354-G-A			Likely benign (Dec 31, 2019)
12-14424360-C-T			Benign (May 09, 2018)
12-14424379-C-T		not specified	Uncertain significance (May 23, 2023)
12-14424441-TCTGGTGATGCCCCTTCTGGTGATGTGTCCC-T			Likely benign (Dec 01, 2023)
12-14424478-A-T		not specified	Uncertain significance (Jun 11, 2021)
12-14424484-C-T		not specified	Uncertain significance (Apr 12, 2022)
12-14424602-A-G		not specified	Uncertain significance (Nov 30, 2021)
12-14424660-C-A		not specified	Uncertain significance (Jan 02, 2024)
12-14424813-G-C		not specified	Uncertain significance (Sep 01, 2021)
12-14424828-A-G		not specified	Uncertain significance (Oct 26, 2022)
12-14424838-C-G		not specified	Uncertain significance (Nov 21, 2022)
12-14424863-T-A		not specified	Uncertain significance (May 01, 2022)
12-14424917-A-T			Benign (Jul 04, 2018)
12-14424942-A-G		not specified	Uncertain significance (Jun 18, 2021)
12-14424954-G-T		not specified	Uncertain significance (Jan 17, 2024)
12-14425003-G-A		not specified	Uncertain significance (Aug 13, 2021)
12-14425051-T-C		not specified	Likely benign (Jul 26, 2022)
12-14425084-T-C		not specified	Uncertain significance (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATF7IP	protein_coding	protein_coding	ENST00000261168	14	133088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000650	125718	0	6	125724	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	543	673	0.807	0.0000337	8282
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000264
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: PKMTs methylate histone lysines;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.155
• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.86

Haploinsufficiency Scores

• pHI: 0.677
• hipred: Y
• hipred_score: 0.519
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.613

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atf7ip

Gene ontology

• 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;regulation of RNA polymerase II transcriptional preinitiation complex assembly
• Cellular component: nucleus;nucleoplasm;transcription factor complex;cytosol;nuclear body
• Molecular function: transcription corepressor activity;protein binding;ATPase activity