TFCP2L1

transcription factor CP2 like 1

Basic information

Region (hg38): 2:121216586-121285202

Links

ENSG00000115112 ∙ NCBI:29842 ∙ OMIM:609785 ∙ HGNC:17925 ∙ Uniprot:Q9NZI6 ∙ 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 TFCP2L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFCP2L1 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					2	2
missense			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	23	0	3

Variants in TFCP2L1

This is a list of pathogenic ClinVar variants found in the TFCP2L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-121224373-C-T		not specified	Uncertain significance (Mar 18, 2024)
2-121231854-G-A		not specified	Uncertain significance (Nov 09, 2023)
2-121231866-C-T		not specified	Uncertain significance (Jul 26, 2022)
2-121231960-C-T		not specified	Uncertain significance (Jul 26, 2022)
2-121234129-T-C		not specified	Uncertain significance (Jan 18, 2022)
2-121235243-G-C		not specified	Uncertain significance (Mar 25, 2024)
2-121235262-A-C			Benign (Jun 15, 2018)
2-121237667-C-T		not specified	Uncertain significance (Jun 16, 2024)
2-121237670-T-C		not specified	Uncertain significance (Jun 07, 2023)
2-121237690-C-G		not specified	Uncertain significance (Nov 14, 2023)
2-121237810-C-A		not specified	Uncertain significance (Jun 04, 2024)
2-121239582-G-C		not specified	Uncertain significance (Dec 19, 2022)
2-121239631-C-T		not specified	Uncertain significance (Sep 22, 2023)
2-121242351-C-T			Benign (May 23, 2018)
2-121242387-G-A		not specified	Uncertain significance (Sep 25, 2023)
2-121242426-A-G		not specified	Uncertain significance (Jun 10, 2024)
2-121242433-C-G		not specified	Uncertain significance (May 06, 2022)
2-121242436-G-A		not specified	Uncertain significance (Jun 16, 2023)
2-121242437-GT-G		Chronic kidney disease	Likely pathogenic (Jan 25, 2021)
2-121246970-C-T		not specified	Uncertain significance (Feb 11, 2022)
2-121248180-G-A		not specified	Uncertain significance (Oct 31, 2022)
2-121249615-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-121249627-G-T		not specified	Uncertain significance (Jan 03, 2024)
2-121249631-G-A			Benign (May 23, 2018)
2-121281142-C-G		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TFCP2L1	protein_coding	protein_coding	ENST00000263707	15	68621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000381	125741	0	2	125743	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	213	291	0.731	0.0000181	3130
Missense in Polyphen		66	121.4	0.54368		1273
Synonymous	0.418	119	125	0.952	0.00000836	904
Loss of Function	5.18	1	33.2	0.0302	0.00000191	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that facilitates establishment and maintenance of pluripotency in embryonic stem cells (ESCs) (PubMed:25215486, PubMed:26906118). With KLF2, acts as the major effector of self-renewal that mediates induction of pluripotency downstream of LIF/STAT3 and Wnt/beta-catenin signaling (By similarity). Required for normal duct development in the salivary gland and kidney (By similarity). Coordinates the development of the kidney collecting ducts intercalated (IC) and principal (PC) cells, which regulate acid-base and salt-water homeostasis, respectively (By similarity). Regulates the expression of IC genes including subunits B1 and D2 of the V-ATPase complex, OXGR1, CA12, SLC4A1, AQP6 and IC-specific transcription factor FOXI1 (By similarity). Regulates also the expression of JAG1 and subsequent notch signaling in the collecting duct (By similarity). JAG1 initiates notch signaling in PCs but inhibits notch signaling in ICs (By similarity). Acts as a transcriptional suppressor that may suppress UBP1-mediated transcriptional activation (By similarity). Modulates the placental expression of CYP11A1 (PubMed:10644752). {ECO:0000250|UniProtKB:Q3UNW5, ECO:0000269|PubMed:10644752, ECO:0000269|PubMed:25215486, ECO:0000269|PubMed:26906118}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.0581
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.85

Haploinsufficiency Scores

• pHI: 0.130
• hipred: Y
• hipred_score: 0.768
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.575

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tfcp2l1
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; digestive/alimentary 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); respiratory system phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;cell morphogenesis;epithelial cell maturation;regulation of transcription by RNA polymerase II;steroid biosynthetic process;cytoplasm organization;salivary gland development;female pregnancy;determination of adult lifespan;positive regulation of growth
• Cellular component: fibrillar center;nucleus;mitochondrion;membrane
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;sequence-specific DNA binding