KLHDC2

kelch domain containing 2

Basic information

Region (hg38): 14:49768130-49786385

Links

ENSG00000165516 ∙ NCBI:23588 ∙ OMIM:611280 ∙ HGNC:20231 ∙ Uniprot:Q9Y2U9 ∙ 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 KLHDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHDC2 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1	7	1	1	10
Total	0	1	23	1	1

Variants in KLHDC2

This is a list of pathogenic ClinVar variants found in the KLHDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-49768487-G-A		not specified	Uncertain significance (Jul 05, 2023)
14-49768561-G-C		not specified	Uncertain significance (May 18, 2022)
14-49768604-G-A		not specified	Uncertain significance (May 05, 2023)
14-49771650-C-G		not specified	Uncertain significance (Jul 05, 2023)
14-49771655-A-G		not specified	Uncertain significance (Jun 09, 2022)
14-49777890-A-G		not specified	Uncertain significance (Jan 08, 2024)
14-49778486-A-G		not specified	Uncertain significance (Dec 15, 2022)
14-49779635-C-T		not specified	Uncertain significance (May 31, 2023)
14-49779655-G-A		not specified	Uncertain significance (Nov 19, 2022)
14-49779773-A-G		not specified	Uncertain significance (Jan 23, 2023)
14-49780214-A-G		not specified	Uncertain significance (Jan 23, 2023)
14-49780256-C-G		not specified	Uncertain significance (Dec 15, 2022)
14-49782395-G-A		not specified	Uncertain significance (Jul 09, 2021)
14-49782593-C-T		not specified	Uncertain significance (Dec 03, 2021)
14-49782879-T-C		not specified	Uncertain significance (May 17, 2023)
14-49782884-C-A		not specified	Uncertain significance (Oct 12, 2021)
14-49784672-C-A			Likely benign (Dec 01, 2022)
14-49784706-T-C		Inborn genetic diseases	Uncertain significance (Oct 27, 2022)
14-49784952-T-C		NEMF-related disorder	Benign (Dec 31, 2019)
14-49784959-G-A		Inborn genetic diseases	Uncertain significance (Nov 18, 2022)
14-49784975-G-A		Inborn genetic diseases	Uncertain significance (Jun 04, 2021)
14-49784976-C-T		Inborn genetic diseases	Uncertain significance (Jun 04, 2021)
14-49784977-A-G		Inborn genetic diseases	Uncertain significance (Jun 13, 2023)
14-49785262-G-A		Inborn genetic diseases	Uncertain significance (Mar 24, 2023)
14-49785298-GTCAAAGAA-G		Intellectual developmental disorder with speech delay and axonal peripheral neuropathy	Likely pathogenic (May 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHDC2	protein_coding	protein_coding	ENST00000298307	13	15584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0265	0.973	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.927	175	213	0.821	0.0000100	2660
Missense in Polyphen		48	73.314	0.65472		874
Synonymous	1.35	57	71.5	0.797	0.00000350	724
Loss of Function	3.41	8	27.2	0.294	0.00000128	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000159	0.000155
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00115	0.00114
Finnish	0.00	0.00
European (Non-Finnish)	0.000260	0.000255
Middle Eastern	0.00115	0.00114
South Asian	0.0000660	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Represses CREB3-mediated transcription by interfering with CREB3-DNA binding. {ECO:0000269|PubMed:11384994}.

Recessive Scores

• pRec: 0.144

Intolerance Scores

• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.33

Haploinsufficiency Scores

• pHI: 0.223
• hipred: Y
• hipred_score: 0.554
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhdc2
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; vision/eye phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Cellular component: nucleus;nuclear body;nuclear membrane