GPBP1L1

protein-coding

GC-rich promoter binding protein 1 like 1

Gene summary

Predicted to enable DNA-binding transcription factor activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_021639.5

Inheritance

—

ClinVar variants

U:61B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr1:45,627,304-45,688,113

External References & Databases

Ensembl (ENSG00000159592)

Transcript & Mutation Effects

hg38 • Region Span ~60.8 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 GPBP1L1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021639.5. 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						0
missense			60 clinvar	1 clinvar		61
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	61	1	0	62

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 105 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021639.5	RefSeq	NP_067652.1	10	MANE Select
ENST00000355105.8	Ensembl	ENSP00000347224.3	10	MANE Select
NM_001439214.1	RefSeq	NP_001426143.1	10	Standard
ENST00000290795.7	Ensembl	ENSP00000290795.3	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transcription, DNA-templated
regulation of transcription, DNA-templated
positive regulation of transcription, DNA-templated

Molecular Function

DNA binding
DNA-binding transcription factor activity

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355105
Coding exons: 10
Length: 60810
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125748
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.133	273	267	1.02	0.0000142	3127
Missense (PolyPhen)		90	80.303	1.1207		1059
Synonymous	-2.18	121	94.1	1.29	0.00000475	914
Loss of Function	3.44	6	24.3	0.247	0.00000136	274

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Possible transcription factor. {ECO:0000305}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.369
RVIS EVS: -0.98
RVIS percentile EVS: 8.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: E
Indispensability score: 0.972

Gene Damage Prediction

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