STKLD1

protein-coding

serine/threonine kinase like domain containing 1

Gene summary

Predicted to enable protein serine/threonine kinase activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf96

MANE transcript

NM_153710.5

Inheritance

ClinVar variants

U:114B:14

Top phenotype

STKLD1-related disorder

gnomAD constraint

pLI —, LoF o/e 1

Max pathogenic AF

—

Genomic locus

chr9:133,376,366-133,406,096

External References & Databases

Ensembl (ENSG00000198870)

Transcript & Mutation Effects

hg38 • Region Span ~29.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

polydactylyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0021003

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to STKLD1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 114

STKLD1-related disorderTotal: 10

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153710.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	4 clinvar		6
missense			109 clinvar	9 clinvar		118
nonsense			3 clinvar	1 clinvar		4
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	114	14	0	128

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153710.5	RefSeq	NP_714921.4	18	MANE Select
ENST00000371957.4	Ensembl	ENSP00000361025.3	18	MANE Select
ENST00001022582.1	Ensembl	ENSP00000692399.1	6	Standard
ENST00001085798.1	Ensembl	ENSP00000755604.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation

Molecular Function

protein serine/threonine kinase activity
ATP binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371957
Coding exons: 18
Length: 28104
Individuals with no LoFs: 125508
Homozygous LoFs: 2
Heterozygous LoFs: 238
Defined: 125748
p: 0.000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0876	378	383	0.987	0.0000208	4420
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0035	0.0031	notable
Latino/Admixed American	0.00048	0.00043	rare
Ashkenazi Jewish	0.0023	0.0023	notable
East Asian	0.00011	0.00011	rare
Finnish	0.0016	0.0015	notable
European (Non-Finnish)	0.00065	0.00063	rare
South Asian	0.0015	0.0014	notable
Other	0.00051	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.67
RVIS percentile EVS: 84.74

Essentials

Essential (gene trap): N