KREMEN2

kringle containing transmembrane protein 2

Basic information

Region (hg38): 16:2964216-2968380

Links

ENSG00000131650 ∙ NCBI:79412 ∙ OMIM:609899 ∙ HGNC:18797 ∙ Uniprot:Q8NCW0 ∙ 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 KREMEN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KREMEN2 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				1		1
missense			39	1	1	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	2	1

Variants in KREMEN2

This is a list of pathogenic ClinVar variants found in the KREMEN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2964570-T-G		not specified	Uncertain significance (Dec 13, 2022)
16-2964582-G-C		not specified	Uncertain significance (Jul 05, 2022)
16-2964584-G-A		not specified	Uncertain significance (Dec 23, 2022)
16-2964859-G-T		not specified	Uncertain significance (Jan 10, 2023)
16-2964897-C-A		not specified	Uncertain significance (Oct 29, 2021)
16-2964927-G-A		not specified	Uncertain significance (Aug 05, 2024)
16-2964997-A-C		not specified	Uncertain significance (Dec 14, 2024)
16-2965005-T-G		not specified	Uncertain significance (Jan 21, 2025)
16-2966150-G-A		not specified	Uncertain significance (Jul 19, 2022)
16-2966174-G-A		not specified	Uncertain significance (Jul 26, 2022)
16-2966183-A-G		not specified	Uncertain significance (Dec 26, 2023)
16-2966213-G-A		not specified	Uncertain significance (Nov 21, 2022)
16-2966343-G-A		not specified	Uncertain significance (Apr 26, 2024)
16-2966376-G-T		not specified	Uncertain significance (Nov 07, 2024)
16-2966377-C-A		not specified	Uncertain significance (Nov 07, 2024)
16-2966408-G-A		not specified	Uncertain significance (Oct 07, 2024)
16-2966649-G-T		Ependymoma	Uncertain significance (Dec 29, 2017)
16-2966660-G-A		not specified	Uncertain significance (Dec 07, 2024)
16-2966682-C-T		not specified	Uncertain significance (Dec 16, 2023)
16-2966955-T-C		not specified	Uncertain significance (Jul 09, 2024)
16-2966993-G-A		not specified	Uncertain significance (Dec 16, 2022)
16-2967040-G-C		not specified	Uncertain significance (Apr 07, 2022)
16-2967050-C-T		not specified	Uncertain significance (Feb 12, 2025)
16-2967053-C-T		not specified	Uncertain significance (Jul 26, 2022)
16-2967062-C-A		not specified	Uncertain significance (Aug 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KREMEN2	protein_coding	protein_coding	ENST00000303746	9	4440

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000372	0.955	125569	0	12	125581	0.0000478

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	178	245	0.728	0.0000156	2836
Missense in Polyphen		62	96.435	0.64292		990
Synonymous	-0.559	122	114	1.07	0.00000812	991
Loss of Function	1.83	10	18.5	0.541	9.22e-7	210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000696	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000264
Middle Eastern	0.000163	0.000163
South Asian	0.000138	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for Dickkopf proteins. Cooperates with DKK1/2 to inhibit Wnt/beta-catenin signaling by promoting the endocytosis of Wnt receptors LRP5 and LRP6. Plays a role in limb development; attenuates Wnt signaling in the developing limb to allow normal limb patterning and can also negatively regulate bone formation. {ECO:0000250|UniProtKB:Q8K1S7}.
• Pathway: WNT-Ncore;Signaling by WNT;Signal Transduction;wnt signaling pathway;segmentation clock;multi-step regulation of transcription by pitx2;wnt lrp6 signalling;inactivation of gsk3 by akt causes accumulation of b-catenin in alveolar macrophages;Negative regulation of TCF-dependent signaling by WNT ligand antagonists;Wnt Canonical;Wnt signaling network;TCF dependent signaling in response to WNT;Wnt Mammals;Presenilin action in Notch and Wnt signaling (Consensus)

Recessive Scores

• pRec: 0.106

Haploinsufficiency Scores

• pHI: 0.165
• hipred: Y
• hipred_score: 0.740
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kremen2
• Phenotype: normal phenotype; limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

• Biological process: Wnt signaling pathway;negative regulation of ossification;limb development;negative regulation of canonical Wnt signaling pathway
• Cellular component: plasma membrane;integral component of membrane;early endosome membrane