SHISAL2A

shisa like 2A

Basic information

Region (hg38): 1:52633167-52669683

Previous symbols: [ "FAM159A" ]

Links

ENSG00000182183 ∙ NCBI:348378 ∙ OMIM:620218 ∙ HGNC:28757 ∙ Uniprot:Q6UWV7 ∙ 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 SHISAL2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHISAL2A 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	2		14
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	2	0

Variants in SHISAL2A

This is a list of pathogenic ClinVar variants found in the SHISAL2A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52633542-C-T		not specified	Uncertain significance (Mar 31, 2024)
1-52633545-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-52633558-C-T		not specified	Uncertain significance (Apr 05, 2023)
1-52633569-G-A		not specified	Uncertain significance (Apr 08, 2024)
1-52633635-A-G		not specified	Uncertain significance (Aug 17, 2022)
1-52633650-G-A		not specified	Uncertain significance (Sep 28, 2022)
1-52633656-A-G		not specified	Uncertain significance (Jun 17, 2024)
1-52633670-G-T		not specified	Uncertain significance (Nov 29, 2023)
1-52642888-G-A		not specified	Likely benign (Feb 10, 2022)
1-52642912-T-C		not specified	Uncertain significance (Jan 18, 2023)
1-52656801-G-T		not specified	Uncertain significance (Mar 28, 2024)
1-52656820-G-T		not specified	Uncertain significance (Jan 04, 2024)
1-52656892-C-T		not specified	Uncertain significance (Nov 27, 2023)
1-52656913-G-A		not specified	Likely benign (Nov 08, 2022)
1-52656915-C-G		not specified	Uncertain significance (Mar 15, 2024)
1-52656918-G-C		not specified	Uncertain significance (May 05, 2023)
1-52656933-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-52656954-A-C		not specified	Uncertain significance (Jun 03, 2022)
1-52656970-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-52657036-C-T		not specified	Uncertain significance (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHISAL2A	protein_coding	protein_coding	ENST00000517870	3	36340

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000512	0.263	124779	0	22	124801	0.0000881

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.278	121	113	1.07	0.00000570	1248
Missense in Polyphen		52	46.096	1.1281		510
Synonymous	-0.184	48	46.4	1.03	0.00000252	372
Loss of Function	-0.345	6	5.16	1.16	2.20e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.000501	0.000501
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000466	0.0000441
Middle Eastern	0.000501	0.000501
South Asian	0.0000335	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.144
• ghis: 0.521

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Shisal2a

Gene ontology

• Cellular component: integral component of membrane