SDF2L1

protein-coding

stromal cell derived factor 2 like 1

Gene summary

Enables misfolded protein binding activity. Involved in protein refolding. Located in endoplasmic reticulum. Part of protein folding chaperone complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_022044.3

Inheritance

—

ClinVar variants

U:36

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr22:21,642,302-21,644,299

External References & Databases

Ensembl (ENSG00000128228)

Transcript & Mutation Effects

hg38 • Region Span ~2.0 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 SDF2L1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 33

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022044.3. 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			34 clinvar			34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	36	0	0	36

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022044.3	RefSeq	NP_071327.2	3	MANE Select
ENST00000248958.5	Ensembl	ENSP00000248958.4	3	MANE Select
ENST00000927919.1	Ensembl	ENSP00000597978.1	3	Standard
ENST00000927919.2	Ensembl	ENSP00000597978.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ibuprofen Action Pathway
Phenytoin (Antiarrhythmic) Action Pathway
Ibuprofen Metabolism Pathway
Morphine Metabolism Pathway
Irinotecan Action Pathway

Biological Process

regulation of apoptotic process
ER-associated misfolded protein catabolic process

Molecular Function

chaperone binding
ATPase binding
misfolded protein binding

Cellular Component

endoplasmic reticulum lumen
membrane
endoplasmic reticulum chaperone complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000248958
Coding exons: 3
Length: 2038
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125732
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.39	78	121	0.644	0.00000672	1388
Missense (PolyPhen)		42	61.294	0.68522		673
Synonymous	0.739	48	55.0	0.873	0.00000336	462
Loss of Function	1.67	2	6.64	0.301	2.86e-7	77

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.125

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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