SAAL1

protein-coding

serum amyloid A like 1, the group of Armadillo like helical domain containing

Gene summary

Acts upstream of or within positive regulation of synoviocyte proliferation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_138421.3

Inheritance

—

ClinVar variants

U:62B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr11:18,069,935-18,106,087

External References & Databases

Ensembl (ENSG00000166788)

Transcript & Mutation Effects

hg38 • Region Span ~36.2 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 SAAL1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 59

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138421.3. 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			56 clinvar	5 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	62	5	0	67

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138421.3	RefSeq	NP_612430.2	12	MANE Select
ENST00000524803.6	Ensembl	ENSP00000432487.1	12	MANE Select
ENST00000300013.8	Ensembl	ENSP00000300013.4	12	Standard
ENST00000300013.9	Ensembl	ENSP00000300013.4	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular space
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000524803
Coding exons: 12
Length: 36157
Individuals with no LoFs: 125690
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125748
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.373	224	240	0.932	0.0000113	3122
Missense (PolyPhen)		63	72.348	0.87079		999
Synonymous	0.205	83	85.4	0.972	0.00000407	840
Loss of Function	1.57	17	25.6	0.665	0.00000115	325

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00051	0.00050	rare
East Asian	0.00027	0.00027	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00010	0.000098	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in promoting the proliferation of synovial fibroblasts in response to proinflammatory stimuli. {ECO:0000269|PubMed:22127701}.;

Recessive Scores

pRec: 0.0927

Intolerance Scores

LoFtool: 0.832
RVIS EVS: 1.13
RVIS percentile EVS: 92.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.621

Gene Damage Prediction

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