CRIPT

CXXC repeat containing interactor of PDZ3 domain

Basic information

Region (hg38): 2:46616416-46685037

Links

ENSG00000119878

∙ NCBI:9419 ∙ OMIM:604594 ∙ HGNC:14312 ∙ Uniprot:Q9P021 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Rothmund-Thomson syndrome, type 3 (Limited), mode of inheritance: AR
Rothmund-Thomson syndrome, type 3 (Moderate), mode of inheritance: AR
Rothmund-Thomson syndrome, type 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Rothmund-Thomson syndrome, type 3	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic	24389050; 27250922

ClinVar

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

not_provided (50 variants)
Inborn_genetic_diseases (17 variants)
Rothmund-Thomson_syndrome_type_3 (9 variants)
CRIPT-related_disorder (3 variants)
Ateleiotic_dwarfism (2 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
not_specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRIPT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014171.6. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				9 clinvar	1 clinvar	10
missense	1 clinvar	1 clinvar	28 clinvar	1 clinvar		31
nonsense	1 clinvar					1
start loss						0
frameshift	5 clinvar					5
splice donor/acceptor (+/-2bp)		2 clinvar				2
Total	7	3	28	10	1

Highest pathogenic variant AF is 0.0000664489

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRIPT	protein_coding	protein_coding	ENST00000238892	5	9327

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000978	0.603	125675	0	10	125685	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.395	57	49.2	1.16	0.00000217	661
Missense in Polyphen		16	17.571	0.91058		235
Synonymous	0.398	14	16.0	0.873	7.58e-7	166
Loss of Function	0.519	5	6.42	0.779	2.69e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000715	0.0000704
Middle Eastern	0.0000556	0.0000544
South Asian	0.00	0.00
Other	0.000175	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in the cytoskeletal anchoring of DLG4 in excitatory synapses. {ECO:0000250|UniProtKB:Q792Q4}.;
Disease: DISEASE: Short stature with microcephaly and distinctive facies (SSMF) [MIM:615789]: A disease characterized by dwarfism, microcephaly, and distinctive facial dysmorphism involving frontal bossing, high forehead, sparse hair and eyebrows, telecanthus, mild proptosis, anteverted nares, and flat nasal bridge. {ECO:0000269|PubMed:24389050, ECO:0000269|PubMed:27250922}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.688
rvis_EVS: -0.12
rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

pHI: 0.148
hipred: Y
hipred_score: 0.679
ghis: 0.660

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cript
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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: cytoplasmic microtubule organization;protein localization to microtubule;establishment of protein localization;regulation of postsynaptic density protein 95 clustering
Cellular component: fibrillar center;nucleus;nucleolus;cytoplasm;postsynaptic density;cell junction;dendrite;neuronal cell body;dendritic spine;dendritic shaft
Molecular function: protein binding;microtubule binding;PDZ domain binding;protein-containing complex binding;scaffold protein binding