CRAMP1

cramped chromatin regulator homolog 1, the group of Myb/SANT domain containing

Basic information

Region (hg38): 16:1612336-1677908

Previous symbols: [ "CRAMP1L" ]

Links

ENSG00000007545 ∙ NCBI:57585 ∙ ∙ HGNC:14122 ∙ Uniprot:Q96RY5 ∙ 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 CRAMP1 gene.

• Inborn genetic diseases (63 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRAMP1 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			58	5		63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	5	0

Variants in CRAMP1

This is a list of pathogenic ClinVar variants found in the CRAMP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1614673-G-A		not specified	Uncertain significance (Jan 18, 2023)
16-1614695-G-A		not specified	Uncertain significance (Jul 14, 2021)
16-1614742-G-A		not specified	Uncertain significance (Oct 26, 2021)
16-1614770-G-A		not specified	Uncertain significance (Nov 27, 2023)
16-1614811-G-A		not specified	Uncertain significance (Feb 28, 2024)
16-1614820-G-A		not specified	Uncertain significance (Mar 23, 2023)
16-1614824-C-T		not specified	Uncertain significance (Dec 21, 2023)
16-1614839-A-C		not specified	Uncertain significance (Jul 09, 2021)
16-1614845-C-T		not specified	Uncertain significance (Dec 01, 2022)
16-1614847-T-G		not specified	Uncertain significance (Sep 15, 2021)
16-1614889-C-T		not specified	Uncertain significance (Nov 09, 2022)
16-1614923-G-A		not specified	Uncertain significance (Oct 04, 2022)
16-1614941-C-T		not specified	Uncertain significance (Oct 18, 2021)
16-1614944-T-C		not specified	Uncertain significance (Oct 30, 2023)
16-1614968-C-T		not specified	Uncertain significance (May 04, 2022)
16-1626057-G-A		not specified	Uncertain significance (Jun 24, 2022)
16-1626096-A-G		not specified	Uncertain significance (Aug 17, 2021)
16-1637880-G-A		not specified	Uncertain significance (Dec 21, 2023)
16-1652516-A-T		not specified	Uncertain significance (Mar 24, 2023)
16-1655280-G-A		not specified	Uncertain significance (Jan 09, 2023)
16-1655299-T-G		not specified	Uncertain significance (May 04, 2023)
16-1655878-G-A		not specified	Uncertain significance (May 27, 2022)
16-1655923-C-T		not specified	Likely benign (Aug 22, 2023)
16-1655936-G-T		not specified	Uncertain significance (Jan 04, 2022)
16-1656045-G-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRAMP1	protein_coding	protein_coding	ENST00000397412	20	65584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0502	0.950	124597	0	45	124642	0.000181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	607	710	0.855	0.0000458	8048
Missense in Polyphen		200	302.36	0.66146		3377
Synonymous	-1.57	355	319	1.11	0.0000226	2685
Loss of Function	4.70	12	46.6	0.257	0.00000228	580

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000783	0.000783
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000890	0.0000885
Middle Eastern	0.00	0.00
South Asian	0.000108	0.0000980
Other	0.000663	0.000661

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.774

Intolerance Scores

• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.34

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.443
• ghis: 0.544

Mouse Genome Informatics

• Gene name: Cramp1l
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;chromatin binding