SAP30L

SAP30 like

Basic information

Region (hg38): 5:154445997-154461053

Links

ENSG00000164576

∙ NCBI:79685 ∙ OMIM:610398 ∙ HGNC:25663 ∙ Uniprot:Q9HAJ7 ∙ 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 SAP30L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAP30L 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			10 clinvar			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in SAP30L

This is a list of pathogenic ClinVar variants found in the SAP30L region.

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

Position	Phenotype	Significance	ClinVar
5-154446640-A-C	not specified	Uncertain significance (Nov 10, 2022)	2393323
5-154446644-C-A	not specified	Uncertain significance (Dec 19, 2022)	2411146
5-154446660-C-T	not specified	Uncertain significance (Jul 26, 2022)	2219019
5-154446704-G-A	not specified	Uncertain significance (Oct 20, 2021)	2255918
5-154446740-T-G	not specified	Uncertain significance (Jun 11, 2024)	3316140
5-154451166-A-G	not specified	Uncertain significance (Jan 26, 2022)	2217576
5-154451208-C-A	not specified	Uncertain significance (Sep 22, 2021)	2387608
5-154451208-C-G	not specified	Uncertain significance (May 30, 2023)	2540548
5-154453456-A-C	not specified	Uncertain significance (Mar 14, 2023)	2496131
5-154455960-A-G	not specified	Uncertain significance (Nov 21, 2022)	2328998
5-154456003-C-T	not specified	Uncertain significance (Jun 29, 2023)	2602367

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAP30L	protein_coding	protein_coding	ENST00000297109	4	15098

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00143	0.881	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.797	78	100	0.776	0.00000509	1214
Missense in Polyphen		18	44.48	0.40468		524
Synonymous	1.56	29	41.8	0.694	0.00000233	325
Loss of Function	1.36	6	10.8	0.554	8.17e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000588	0.0000588
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000668	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Isoform 1: Functions as transcription repressor, probably via its interaction with histone deacetylase complexes (PubMed:16820529, PubMed:18070604). Involved in the functional recruitment of the class 1 Sin3-histone deacetylase complex (HDAC) to the nucleolus (PubMed:16820529). Binds DNA, apparently without sequence-specificity, and bends bound double-stranded DNA (PubMed:19015240). Binds phosphoinositol phosphates (phosphoinositol 3-phosphate, phosphoinositol 4-phosphate and phosphoinositol 5-phosphate) via the same basic sequence motif that mediates DNA binding and nuclear import (PubMed:19015240, PubMed:26609676). {ECO:0000269|PubMed:16820529, ECO:0000269|PubMed:18070604, ECO:0000269|PubMed:19015240, ECO:0000269|PubMed:26609676}.; FUNCTION: Isoform 3: Functions as transcription repressor; its activity is marginally lower than that of isoform 1. {ECO:0000269|PubMed:18070604}.;
Pathway: NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);HDACs deacetylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.111
rvis_EVS: -0.01
rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

pHI: 0.313
hipred: Y
hipred_score: 0.719
ghis: 0.505

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Sap30l
Phenotype

Zebrafish Information Network

Gene name: sap30l
Affected structure: heart
Phenotype tag: abnormal
Phenotype quality: morphology

Gene ontology

Biological process: regulation of transcription, DNA-templated;histone deacetylation
Cellular component: histone deacetylase complex;nucleus;nucleoplasm;nucleolus
Molecular function: DNA binding;histone deacetylase activity;protein binding;zinc ion binding;phosphatidylinositol-5-phosphate binding;nucleosome binding;histone binding;non-sequence-specific DNA binding, bending