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.

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.

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		1
missense			37	6		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	7	0

Variants in ATF7IP2

This is a list of pathogenic ClinVar variants found in the ATF7IP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-10430630-C-A		not specified	Uncertain significance (Apr 26, 2023)
16-10430645-C-T		not specified	Uncertain significance (May 20, 2024)
16-10430687-C-T		not specified	Uncertain significance (Apr 18, 2024)
16-10430688-G-A		not specified	Uncertain significance (Mar 18, 2024)
16-10430699-G-A		not specified	Uncertain significance (Aug 09, 2021)
16-10430733-T-C		not specified	Uncertain significance (Aug 09, 2021)
16-10430751-G-A		not specified	Likely benign (Dec 14, 2023)
16-10430792-A-G		not specified	Uncertain significance (Dec 27, 2022)
16-10430796-C-G		not specified	Likely benign (Mar 17, 2023)
16-10430802-C-T		not specified	Uncertain significance (Aug 12, 2021)
16-10430826-C-A		not specified	Likely benign (May 01, 2024)
16-10430841-C-T		not specified	Uncertain significance (Oct 26, 2021)
16-10430870-A-G		not specified	Likely benign (Nov 14, 2023)
16-10430958-T-A		not specified	Uncertain significance (Jan 09, 2024)
16-10430964-C-T		not specified	Uncertain significance (Nov 14, 2023)
16-10431020-G-T		not specified	Uncertain significance (Sep 12, 2023)
16-10431071-G-A		not specified	Likely benign (Nov 21, 2022)
16-10431090-A-G		not specified	Uncertain significance (Jul 25, 2023)
16-10431092-C-T		not specified	Uncertain significance (Oct 22, 2021)
16-10431101-G-A		not specified	Uncertain significance (Apr 29, 2024)
16-10431179-A-G		not specified	Uncertain significance (Mar 20, 2024)
16-10431180-G-A		not specified	Likely benign (Feb 28, 2023)
16-10431250-T-A		not specified	Uncertain significance (Mar 04, 2024)
16-10431287-G-C		not specified	Uncertain significance (Jul 27, 2023)
16-10431339-C-T		not specified	Likely benign (Jan 07, 2022)

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