SMARCAL1

Protein identityUniProt · HPA

UniProt accession

Q9NZC9

Gene

SMARCAL1

Ensembl

ENSG00000138375

Chromosome

2

Canonical length

954 aa

Protein class

Disease related genes, Human disease related genes, Predicted intracellular proteins

Subcellular location

Nucleoplasm

OverviewNCBI Gene

The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein shows sequence similarity to the E. coli RNA polymerase-binding protein HepA. Mutations in this gene are a cause of Schimke immunoosseous dysplasia (SIOD), an autosomal recessive disorder with the diagnostic features of spondyloepiphyseal dysplasia, renal dysfunction, and T-cell immunodeficiency. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

954 residues, UniProt reviewed canonical sequence.

>Q9NZC9|SMARCAL1
     1  MSLPLTEEQR KKIEENRQKA LARRAEKLLA EQHQRTSSGT SIAGNPFQAK QGPSQNFPRE
    61  SCKPVSHGVI FKQQNLSSSS NADQRPHDSH SFQAKGIWKK PEEMPTACPG HSPRSQMALT
   121  GISPPLAQSP PEVPKQQLLS YELGQGHAQA SPEIRFTPFA NPTHKPLAKP KSSQETPAHS
   181  SGQPPRDAKL EAKTAKASPS GQNISYIHSS SESVTPRTEG RLQQKSGSSV QKGVNSQKGK
   241  CVRNGDRFQV LIGYNAELIA VFKTLPSKNY DPDTKTWNFS MNDYSALMKA AQSLPTVNLQ
   301  PLEWAYGSSE SPSTSSEGQA GLPSAPSLSF VKGRCMLISR AYFEADISYS QDLIALFKQM
   361  DSRRYDVKTR KWSFLLEEHS KLIAKVRCLP QVQLDPLPTT LTLAFASQLK KTSLSLTPDV
   421  PEADLSEVDP KLVSNLMPFQ RAGVNFAIAK GGRLLLADDM GLGKTIQAIC IAAFYRKEWP
   481  LLVVVPSSVR FTWEQAFLRW LPSLSPDCIN VVVTGKDRLT AGLINIVSFD LLSKLEKQLK
   541  TPFKVVIIDE SHFLKNSRTA RCRAAMPVLK VAKRVILLSG TPAMSRPAEL YTQIIAVKPT
   601  FFPQFHAFGL RYCDAKRMPW GWDYSGSSNL GELKLLLEEA VMLRRLKSDV LSQLPAKQRK
   661  IVVIAPGRIN ARTRAALDAA AKEMTTKDKT KQQQKDALIL FFNRTAEAKI PSVIEYILDL
   721  LESGREKFLV FAHHKVVLDA ITQELERKHV QHIRIDGSTS SAEREDLCQQ FQLSERHAVA
   781  VLSITAANMG LTFSSADLVV FAELFWNPGV LIQAEDRVHR IGQTSSVGIH YLVAKGTADD
   841  YLWPLIQEKI KVLAEAGLSE TNFSEMTEST DYLYKDPKQQ KIYDLFQKSF EKEGSDMELL
   901  EAAESFDPGS ASGTSGSSSQ NMGDTLDESS LTASPQKKRR FEFFDNWDSF TSPL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SMARCAL1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Intracellular

Secreted

No

Transmembrane segments

0

Mean surface accessibility (rSASA)

0.4

Highest tissue expression

12 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SMARCAL1.

Disease | AllUniProt

Conditions SMARCAL1 is implicated in, by any mechanism.

• Schimke immuno-osseous dysplasia (SIOD) MIM:242900

Disease | GeneticClinVar

167 pathogenic / likely-pathogenic of 1,365 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Schimke immuno-osseous dysplasia
• Nephrotic syndrome
• 9 conditions
• See cases
• SMARCAL1-related disorder

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

0.61

gnomAD pLI

0

gnomAD missense Z

0.84

DepMap mean gene effect

0.04

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 7% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• DNA damage response
• DNA repair
• double-strand break repair via nonhomologous end joining
• regulation of transcription by RNA polymerase II
• replication fork processing
• t-circle formation

Molecular functions

• ATP binding
• ATP hydrolysis activity
• ATP-dependent DNA/DNA annealing activity

Cellular components

• nuclear replication fork
• nucleoplasm
• nucleus
• site of double-strand break

Protein domainsUniProt · Pfam · InterPro

• SNF2, N-terminal domain
• Helicase, C-terminal domain-like
• Helicase superfamily 1/2, ATP-binding domain
• P-loop containing nucleoside triphosphate hydrolase
• SNF2-like, N-terminal domain superfamily
• SNF2/RAD5-like, C-terminal helicase domain
• SNF2-related domain
• Helicase conserved C-terminal domain
• HARP domain
• HepA-related protein (HARP)

KeywordsUniProt

• Acetylation
• Coiled coil
• Hydrolase
• Isomerase
• Nucleus
• Phosphoprotein
• Repeat

InteractionsUniProt · HPA

Protein binding partners of SMARCAL1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• RPA2