SAAL1

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

Basic information

Region (hg38): 11:18069935-18106087

Links

ENSG00000166788 ∙ NCBI:113174 ∙ ∙ HGNC:25158 ∙ Uniprot:Q96ER3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAAL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAAL1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in SAAL1

This is a list of pathogenic ClinVar variants found in the SAAL1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-18080466-C-T		not specified	Likely benign (Feb 13, 2025)
11-18081419-T-C		not specified	Uncertain significance (Apr 13, 2023)
11-18081430-A-G		not specified	Uncertain significance (Aug 27, 2024)
11-18081472-T-C		not specified	Uncertain significance (Dec 30, 2024)
11-18083579-T-C		not specified	Uncertain significance (Aug 12, 2021)
11-18083593-T-C		not specified	Uncertain significance (Nov 21, 2023)
11-18083602-A-C		not specified	Uncertain significance (Aug 01, 2024)
11-18083626-C-T		not specified	Likely benign (May 04, 2023)
11-18083661-C-A		not specified	Uncertain significance (Nov 21, 2024)
11-18086944-C-G		not specified	Uncertain significance (Jan 01, 2025)
11-18086968-T-G		not specified	Uncertain significance (Dec 31, 2024)
11-18086970-G-C		not specified	Uncertain significance (Sep 10, 2024)
11-18086997-T-A		not specified	Uncertain significance (Jun 25, 2024)
11-18087048-C-T		not specified	Uncertain significance (Jan 26, 2025)
11-18087205-A-T		not specified	Uncertain significance (Oct 28, 2024)
11-18089339-T-C		not specified	Uncertain significance (Feb 22, 2023)
11-18089355-T-C		not specified	Likely benign (Sep 29, 2022)
11-18089391-A-G		not specified	Uncertain significance (Feb 05, 2024)
11-18089399-T-G		not specified	Uncertain significance (Dec 02, 2024)
11-18089409-C-G		not specified	Uncertain significance (Oct 24, 2024)
11-18089436-C-A		not specified	Uncertain significance (Jan 23, 2024)
11-18089493-C-A		not specified	Uncertain significance (Jun 28, 2023)
11-18090187-T-C		not specified	Uncertain significance (Mar 18, 2024)
11-18090198-A-G		not specified	Uncertain significance (Nov 03, 2022)
11-18090450-G-C		not specified	Uncertain significance (Oct 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAAL1	protein_coding	protein_coding	ENST00000524803	12	36157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.32e-9	0.812	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.373	224	240	0.932	0.0000113	3122
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000276
Ashkenazi Jewish	0.000510	0.000496
East Asian	0.000272	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000285	0.000281
Middle Eastern	0.000272	0.000272
South Asian	0.000103	0.0000980
Other	0.000501	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.291
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.621

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Saal1

Gene ontology

• Cellular component: extracellular space;nucleus