SPRING1

protein-coding

SREBF pathway regulator in golgi 1

Gene summary

Involved in positive regulation of SREBP signaling pathway. Located in Golgi membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C12orf49

MANE transcript

NM_024738.4

Inheritance

—

ClinVar variants

U:7B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr12:116,710,171-116,738,070

External References & Databases

Ensembl (ENSG00000111412)

Transcript & Mutation Effects

hg38 • Region Span ~27.9 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 SPRING1 variants in ClinVar

1 Conditions Cataloged

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024738.4. 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			1 clinvar	1 clinvar	1 clinvar	3
missense			3 clinvar			3
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	7	1	1	9

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024738.4	RefSeq	NP_079014.1	5	MANE Select
ENST00000261318.5	Ensembl	ENSP00000261318.3	5	MANE Select
NM_001353623.2	RefSeq	NP_001340552.1	4	Standard
NM_001353624.2	RefSeq	NP_001340553.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261318
Coding exons: 5
Length: 22283
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.749	100	123	0.810	0.00000737	1352
Missense (PolyPhen)		29	34.759	0.83433		397
Synonymous	-0.134	52	50.8	1.02	0.00000324	374
Loss of Function	1.51	5	10.2	0.489	4.35e-7	118

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.539
RVIS EVS: 0.19
RVIS percentile EVS: 67.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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