CENPS-CORT

CENPS-CORT readthrough

Basic information

Region (hg38): 1:10430102-10452153

Previous symbols: [ "APITD1-CORT" ]

Links

ENSG00000251503 ∙ NCBI:100526739 ∙ ∙ HGNC:38843 ∙ ∙ ∙ 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 CENPS-CORT gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPS-CORT 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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	5	1	0

Variants in CENPS-CORT

This is a list of pathogenic ClinVar variants found in the CENPS-CORT region.

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

Position	Type	Phenotype	Significance	ClinVar
1-10430528-A-C		not specified	Uncertain significance (Jun 26, 2023)
1-10430542-G-A		not specified	Uncertain significance (Feb 10, 2022)
1-10433906-A-G		not specified	Uncertain significance (Feb 03, 2022)
1-10433933-C-T		not specified	Uncertain significance (May 01, 2024)
1-10434664-T-G		not specified	Uncertain significance (May 07, 2024)
1-10440352-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-10440380-T-A		not specified	Uncertain significance (Feb 26, 2024)
1-10450243-T-G		not specified	Uncertain significance (Apr 25, 2023)
1-10450270-C-T		not specified	Uncertain significance (Nov 30, 2022)
1-10450312-G-A		not specified	Likely benign (Feb 08, 2023)
1-10451504-G-A		not specified	Uncertain significance (Jan 06, 2023)
1-10451512-G-A		not specified	Uncertain significance (Jun 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPS-CORT	protein_coding	protein_coding	ENST00000400900	5	22052

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000575	0.269	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.11	116	86.9	1.33	0.00000418	1078
Missense in Polyphen		24	22.34	1.0743		294
Synonymous	0.510	30	33.8	0.888	0.00000188	291
Loss of Function	0.0245	8	8.07	0.991	4.28e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000614	0.000614
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.0000544	0.0000544
South Asian	0.000132	0.000131
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA-binding component of the Fanconi anemia (FA) core complex. Required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage (PubMed:20347428, PubMed:20347429). In complex with CENPX (MHF heterodimer), crucial cofactor for FANCM in both binding and ATP-dependent remodeling of DNA. Stabilizes FANCM (PubMed:20347428, PubMed:20347429). In complex with CENPX and FANCM (but not other FANC proteins), rapidly recruited to blocked forks and promotes gene conversion at blocked replication forks (PubMed:20347428). In complex with CENPT, CENPW and CENPX (CENP-T-W-S-X heterotetramer), involved in the formation of a functional kinetochore outer plate, which is essential for kinetochore-microtubule attachment and faithful mitotic progression (PubMed:19620631). As a component of MHF and CENP-T-W-S-X complexes, binds DNA and bends it to form a nucleosome-like structure (PubMed:20347428, PubMed:22304917). DNA- binding function is fulfilled in the presence of CENPX, with the following preference for DNA substates: Holliday junction > double-stranded > splay arm > single-stranded. Does not bind DNA on its own (PubMed:20347428, PubMed:20347429). {ECO:0000269|PubMed:19620631, ECO:0000269|PubMed:20347428, ECO:0000269|PubMed:20347429, ECO:0000269|PubMed:22304917}.
• Pathway: Fanconi anemia pathway - Homo sapiens (human);Fanconi Anemia Pathway;DNA Repair;Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;Nucleosome assembly;RHO GTPase Effectors;Signaling by Rho GTPases;Chromosome Maintenance;Fanconi anemia pathway;Deposition of new CENPA-containing nucleosomes at the centromere;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.394