ATF7IP2

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

Basic information

Region (hg38): 16:10326434-10483638

Links

ENSG00000166669 ∙ NCBI:80063 ∙ OMIM:613645 ∙ HGNC:20397 ∙ Uniprot:Q5U623 ∙ 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 ATF7IP2 gene.

• not_specified (96 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATF7IP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001393719.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			86	11		97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	86	12	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATF7IP2	protein_coding	protein_coding	ENST00000396560	10	157205

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.158	0.842	125718	0	10	125728	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.32	409	341	1.20	0.0000163	4496
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000958	0.0000924
European (Non-Finnish)	0.0000448	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000776	0.0000653
Other	0.000175	0.000163

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. 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

Haploinsufficiency Scores

• pHI: 0.0658
• hipred: Y
• hipred_score: 0.519
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.710

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atf7ip2

Gene ontology

• Cellular component: nucleus