SHISAL1

shisa like 1

Basic information

Region (hg38): 22:44243665-44312951

Previous symbols: [ "KIAA1644" ]

Links

ENSG00000138944 ∙ NCBI:85352 ∙ OMIM:620220 ∙ HGNC:29335 ∙ Uniprot:Q3SXP7 ∙ 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 SHISAL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHISAL1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in SHISAL1

This is a list of pathogenic ClinVar variants found in the SHISAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-44285437-G-C		not specified	Uncertain significance (Jan 31, 2022)
22-44285458-G-A		not specified	Uncertain significance (May 18, 2022)
22-44285492-C-T		not specified	Uncertain significance (Dec 03, 2021)
22-44285501-G-C		not specified	Uncertain significance (Apr 19, 2023)
22-44285506-T-G		not specified	Uncertain significance (Mar 20, 2024)
22-44285554-G-A		not specified	Uncertain significance (Apr 04, 2023)
22-44285598-T-A		not specified	Uncertain significance (Mar 23, 2023)
22-44285606-A-G		not specified	Uncertain significance (Jan 23, 2023)
22-44285626-C-T		not specified	Uncertain significance (Jul 14, 2022)
22-44285635-T-C		not specified	Uncertain significance (Aug 08, 2022)
22-44296717-A-G		not specified	Uncertain significance (Aug 28, 2023)
22-44296834-C-A		not specified	Uncertain significance (May 16, 2022)
22-44300920-A-C		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHISAL1	protein_coding	protein_coding	ENST00000381176	3	69185

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0398	0.933	124790	0	6	124796	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.206	127	134	0.950	0.00000914	1284
Missense in Polyphen		31	49.773	0.62282		556
Synonymous	-0.293	64	61.1	1.05	0.00000457	394
Loss of Function	1.91	4	10.8	0.372	5.57e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.613
• ghis: 0.565

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Shisal1

Gene ontology

• Cellular component: integral component of membrane