STKLD1

serine/threonine kinase like domain containing 1

Basic information

Region (hg38): 9:133376366-133406096

Previous symbols: [ "C9orf96" ]

Links

ENSG00000198870 ∙ NCBI:169436 ∙ OMIM:618530 ∙ HGNC:28669 ∙ Uniprot:Q8NE28 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• polydactyly (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STKLD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STKLD1 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			61	2		63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	61	2	0

Variants in STKLD1

This is a list of pathogenic ClinVar variants found in the STKLD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-133376486-G-A		not specified	Uncertain significance (Sep 25, 2024)
9-133376508-C-T		not specified	Uncertain significance (Dec 27, 2023)
9-133376532-C-T		not specified	Uncertain significance (Oct 08, 2024)
9-133376535-C-T		not specified	Uncertain significance (Mar 14, 2023)
9-133376543-C-T		not specified	Uncertain significance (Mar 01, 2024)
9-133376557-C-A			Uncertain significance (Aug 13, 2019)
9-133379046-A-G		STKLD1-related disorder	Likely benign (Jul 28, 2022)
9-133383880-G-A		not specified	Uncertain significance (Jan 23, 2024)
9-133383883-A-G		not specified	Uncertain significance (Jun 10, 2024)
9-133385643-C-G		not specified	Uncertain significance (Aug 10, 2023)
9-133385671-T-C		not specified	Uncertain significance (Jun 24, 2022)
9-133385686-G-A		not specified	Uncertain significance (Jun 16, 2024)
9-133387536-C-G		not specified	Uncertain significance (May 11, 2022)
9-133387542-C-G		not specified	Uncertain significance (Jan 24, 2023)
9-133389560-C-T		not specified	Uncertain significance (Mar 18, 2024)
9-133389566-A-T		not specified	Uncertain significance (Apr 13, 2023)
9-133390681-G-C		not specified	Uncertain significance (Oct 18, 2024)
9-133390721-C-A		not specified	Uncertain significance (Jan 09, 2024)
9-133390758-T-A		not specified	Uncertain significance (Aug 30, 2021)
9-133390787-G-A		not specified	Uncertain significance (Feb 28, 2024)
9-133390788-C-T		not specified	Uncertain significance (Nov 13, 2023)
9-133394292-C-T		STKLD1-related disorder	Likely benign (Nov 05, 2021)
9-133394300-G-A		STKLD1-related disorder	Uncertain significance (Jun 06, 2024)
9-133394311-A-T		not specified	Uncertain significance (Apr 26, 2023)
9-133394321-A-T		not specified	Uncertain significance (Feb 22, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STKLD1	protein_coding	protein_coding	ENST00000371957	18	28104

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-23	0.000665	125508	2	238	125748	0.000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0876	378	383	0.987	0.0000208	4420
Missense in Polyphen		86	87.344	0.98461		1074
Synonymous	-1.19	189	169	1.12	0.0000102	1350
Loss of Function	0.00530	35	35.0	0.999	0.00000156	395

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00398	0.00356
Ashkenazi Jewish	0.00229	0.00228
East Asian	0.000109	0.000109
Finnish	0.00159	0.00148
European (Non-Finnish)	0.000649	0.000633
Middle Eastern	0.000109	0.000109
South Asian	0.00153	0.00141
Other	0.000512	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.74

Haploinsufficiency Scores

• pHI: 0.0926
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Stkld1

Gene ontology

• Biological process: protein phosphorylation
• Molecular function: protein serine/threonine kinase activity;ATP binding