CORO7-PAM16

CORO7-PAM16 readthrough

Basic information

Region (hg38): 16:4340251-4420494

Links

ENSG00000103426 ∙ NCBI:100529144 ∙ ∙ HGNC:44424 ∙ ∙ ∙ 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 CORO7-PAM16 gene.

• not provided (66 variants)
• Inborn genetic diseases (50 variants)
• Autosomal recessive spondylometaphyseal dysplasia, Megarbane type (3 variants)
• Acute megakaryocytic leukemia;Mediastinal germ cell tumor (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CORO7-PAM16 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	10	1	12
missense	2		21		4	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1	2	3
splice region						0
non coding			46	14	17	77
Total	2	0	68	25	24

Variants in CORO7-PAM16

This is a list of pathogenic ClinVar variants found in the CORO7-PAM16 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-4340322-C-T			Likely benign (Aug 02, 2023)
16-4340323-G-A		not specified	Uncertain significance (Oct 18, 2022)
16-4340342-T-C			Uncertain significance (Oct 05, 2022)
16-4340352-C-T			Likely benign (Oct 22, 2023)
16-4340357-G-C			Uncertain significance (Apr 24, 2021)
16-4340357-G-T			Benign (Jan 31, 2024)
16-4340385-G-A			Likely benign (Nov 27, 2020)
16-4340387-G-A			Uncertain significance (Oct 26, 2022)
16-4340390-C-T			Uncertain significance (Aug 16, 2022)
16-4340397-G-A			Likely benign (Dec 25, 2022)
16-4340398-C-T			Uncertain significance (Oct 18, 2022)
16-4340414-T-A			Likely benign (Jul 19, 2022)
16-4340415-C-T			Likely benign (Jul 07, 2023)
16-4340417-C-T			Benign (Jan 18, 2024)
16-4340418-G-A			Likely benign (Jan 13, 2023)
16-4340421-T-C			Likely benign (Oct 27, 2023)
16-4340425-C-G			Likely benign (Dec 06, 2023)
16-4340646-C-C			Benign (Jul 09, 2018)
16-4340872-A-G			Benign (Jul 09, 2018)
16-4340910-G-A			Benign (Jan 18, 2024)
16-4340913-C-A		PAM16-related disorder	Benign/Likely benign (Nov 01, 2024)
16-4340943-C-T			Uncertain significance (Nov 23, 2021)
16-4340948-A-G			Uncertain significance (Jul 12, 2021)
16-4340958-C-G		not specified	Uncertain significance (Jan 31, 2024)
16-4340969-A-C			Uncertain significance (Jun 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CORO7-PAM16	protein_coding	protein_coding	ENST00000572467	31	80244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.62e-25	0.260	125446	1	301	125748	0.00120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.404	687	658	1.04	0.0000436	6620
Missense in Polyphen		245	248.87	0.98447		2467
Synonymous	-1.06	312	289	1.08	0.0000198	2227
Loss of Function	1.96	47	63.9	0.735	0.00000355	632

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00265	0.00257
Ashkenazi Jewish	0.00231	0.00228
East Asian	0.000773	0.000761
Finnish	0.00119	0.00111
European (Non-Finnish)	0.00157	0.00153
Middle Eastern	0.000773	0.000761
South Asian	0.000577	0.000555
Other	0.000345	0.000326

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.270
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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