INTS12

integrator complex subunit 12, the group of PHD finger proteins|Integrator complex

Basic information

Region (hg38): 4:105682626-105895986

Previous symbols: [ "PHF22" ]

Links

ENSG00000138785 ∙ NCBI:57117 ∙ OMIM:611355 ∙ HGNC:25067 ∙ Uniprot:Q96CB8 ∙ 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 INTS12 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INTS12 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	0

Variants in INTS12

This is a list of pathogenic ClinVar variants found in the INTS12 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-105682785-T-C		not specified	Uncertain significance (May 08, 2023)
4-105682891-C-T		not specified	Uncertain significance (Feb 15, 2023)
4-105682913-C-T			Likely benign (Mar 01, 2022)
4-105682939-G-C		not specified	Uncertain significance (May 04, 2023)
4-105682944-A-G		not specified	Uncertain significance (Mar 01, 2024)
4-105682980-T-C		not specified	Uncertain significance (Jul 26, 2021)
4-105683317-T-C		not specified	Uncertain significance (Aug 08, 2023)
4-105686697-C-T		not specified	Uncertain significance (Jun 07, 2023)
4-105686816-G-A		not specified	Uncertain significance (Aug 23, 2021)
4-105692070-C-T		not specified	Likely benign (Feb 23, 2023)
4-105693419-T-C		not specified	Likely benign (Dec 06, 2022)
4-105693486-T-A		not specified	Uncertain significance (Jun 28, 2023)
4-105695520-T-A		not specified	Uncertain significance (Oct 12, 2022)
4-105695551-C-A		not specified	Uncertain significance (Sep 16, 2021)
4-105695610-T-C		not specified	Uncertain significance (Jun 07, 2023)
4-105695617-C-T		not specified	Uncertain significance (Sep 27, 2022)
4-105695649-A-G		not specified	Uncertain significance (Feb 15, 2023)
4-105699863-C-T		not specified	Uncertain significance (Apr 05, 2023)
4-105699894-A-G		not specified	Uncertain significance (Feb 15, 2023)
4-105699971-A-G		not specified	Uncertain significance (Sep 29, 2023)
4-105717756-T-C		not specified	Uncertain significance (Oct 26, 2022)
4-105717789-A-G		not specified	Uncertain significance (Mar 17, 2023)
4-105717887-G-A		not specified	Uncertain significance (Nov 02, 2023)
4-105717909-A-G		not specified	Uncertain significance (Mar 20, 2023)
4-105717973-C-A		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INTS12	protein_coding	protein_coding	ENST00000451321	6	213360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.754	0.246	125736	0	9	125745	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	178	236	0.753	0.0000116	2986
Missense in Polyphen		51	76.311	0.66832		1007
Synonymous	-1.19	100	85.9	1.16	0.00000441	946
Loss of Function	3.25	3	17.8	0.169	9.83e-7	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the Integrator complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (PubMed:16239144). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:16239144, ECO:0000269|PubMed:23904267}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.481
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.684
• hipred: Y
• hipred_score: 0.581
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ints12
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: snRNA processing;snRNA transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;integrator complex
• Molecular function: protein binding;metal ion binding