CRAMP1

protein-coding

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

Gene summary

Enables DNA-binding transcription factor activity. Involved in positive regulation of DNA-templated transcription. Is active in histone locus body. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CRAMP1L

MANE transcript

NM_020825.4

Inheritance

—

ClinVar variants

U:214B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr16:1,612,337-1,677,908

External References & Databases

Ensembl (ENSG00000007545)

Transcript & Mutation Effects

hg38 • Region Span ~65.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CRAMP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 216

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020825.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	1 clinvar		5
missense			208 clinvar	11 clinvar		219
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	214	12	0	226

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020825.4	RefSeq	NP_065876.3	20	MANE Select
ENST00000397412.8	Ensembl	ENSP00000380559.2	20	MANE Select
ENST00000293925.9	Ensembl	ENSP00000293925.5	20	Standard
ENST00000415022.1	Ensembl	ENSP00000399172.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
chromatin binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397412
Coding exons: 20
Length: 65584
Individuals with no LoFs: 124597
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 124642
p: 0.000181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.37	607	710	0.855	0.0000458	8048
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00078	0.00078	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.00011	0.000098	rare
Other	0.00066	0.00066	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.774

Intolerance Scores

RVIS EVS: -1.26
RVIS percentile EVS: 5.34