KRCC1

lysine rich coiled-coil 1

Basic information

Region (hg38): 2:88027205-88064252

Links

ENSG00000172086 ∙ NCBI:51315 ∙ ∙ HGNC:28039 ∙ Uniprot:Q9NPI7 ∙ 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 KRCC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRCC1 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			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in KRCC1

This is a list of pathogenic ClinVar variants found in the KRCC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-88027869-C-T		not specified	Uncertain significance (May 31, 2024)
2-88027888-C-T		not specified	Uncertain significance (Feb 11, 2025)
2-88027903-T-C		not specified	Uncertain significance (May 17, 2023)
2-88027956-T-C		not specified	Uncertain significance (Oct 12, 2022)
2-88028041-G-A		not specified	Uncertain significance (Jun 12, 2023)
2-88028049-T-G		not specified	Uncertain significance (Mar 15, 2023)
2-88028079-C-T		not specified	Uncertain significance (Feb 27, 2024)
2-88028109-C-G		not specified	Uncertain significance (May 03, 2023)
2-88028119-G-A		not specified	Uncertain significance (Mar 07, 2025)
2-88028143-A-G		not specified	Uncertain significance (Jun 11, 2024)
2-88028173-C-T		not specified	Likely benign (Jun 02, 2024)
2-88028175-T-C		not specified	Uncertain significance (Jan 23, 2024)
2-88028242-T-C		not specified	Uncertain significance (Apr 19, 2024)
2-88028262-A-G		not specified	Uncertain significance (Nov 17, 2023)
2-88028313-C-T		not specified	Likely benign (Dec 20, 2023)
2-88028329-G-T		not specified	Uncertain significance (May 18, 2023)
2-88028331-G-A		not specified	Uncertain significance (Aug 26, 2022)
2-88028337-T-C		not specified	Likely benign (Sep 03, 2024)
2-88028379-C-A		not specified	Uncertain significance (Oct 20, 2024)
2-88028427-T-A		not specified	Uncertain significance (Jul 05, 2023)
2-88028446-A-G		not specified	Uncertain significance (May 16, 2022)
2-88028494-C-T		not specified	Uncertain significance (Mar 11, 2022)
2-88028511-T-A		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KRCC1	protein_coding	protein_coding	ENST00000347055	1	28525

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000679	0.761	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.697	110	133	0.830	0.00000676	1722
Missense in Polyphen		18	26.837	0.67073		400
Synonymous	0.0538	46	46.5	0.990	0.00000236	436
Loss of Function	0.986	6	9.23	0.650	4.76e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000919	0.0000914
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.471
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

• pHI: 0.273
• hipred: N
• hipred_score: 0.132
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.516

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Krcc1