CCDC169-SOHLH2

CCDC169-SOHLH2 readthrough

Basic information

Region (hg38): 13:36168794-36297842

Previous symbols: [ "C13orf38-SOHLH2" ]

Links

ENSG00000250709 ∙ NCBI:100526761 ∙ ∙ HGNC:38866 ∙ ∙ ∙ 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 CCDC169-SOHLH2 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC169-SOHLH2 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	3	0	0

Variants in CCDC169-SOHLH2

This is a list of pathogenic ClinVar variants found in the CCDC169-SOHLH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-36170537-G-T		not specified	Uncertain significance (Apr 13, 2022)
13-36170583-C-T		CCDC169-SOHLH2-related disorder	Likely benign (Mar 05, 2019)
13-36170584-G-A		not specified	Uncertain significance (Oct 06, 2021)
13-36170653-C-G		not specified	Uncertain significance (Jan 16, 2024)
13-36170662-C-T		not specified	Uncertain significance (May 25, 2022)
13-36170663-G-A		CCDC169-SOHLH2-related disorder	Benign (Nov 08, 2019)
13-36170721-G-A		not specified	Uncertain significance (May 24, 2023)
13-36170721-G-C		not specified	Uncertain significance (Dec 06, 2021)
13-36170739-G-C		not specified	Uncertain significance (Mar 07, 2024)
13-36170769-G-A		not specified	Uncertain significance (Mar 23, 2022)
13-36170773-C-T		SOHLH2-related disorder	Benign (Oct 25, 2019)
13-36170783-T-C		SOHLH2-related disorder	Likely benign (Mar 01, 2019)
13-36173727-G-A		not specified	Uncertain significance (May 30, 2023)
13-36173749-A-G		not specified	Uncertain significance (Sep 01, 2021)
13-36173751-G-A		not specified	Uncertain significance (Dec 16, 2023)
13-36173782-G-A		not specified	Uncertain significance (Feb 17, 2022)
13-36173786-G-A		SOHLH2-related disorder	Likely benign (Mar 12, 2019)
13-36174733-C-T		not specified	Likely benign (Aug 09, 2021)
13-36174820-C-T		SOHLH2-related disorder	Likely benign (Jul 11, 2023)
13-36174835-T-A		not specified	Uncertain significance (Jun 12, 2023)
13-36189977-G-A		not specified	Uncertain significance (Nov 01, 2024)
13-36189990-G-T		not specified	Uncertain significance (Mar 01, 2023)
13-36189998-C-T		not specified	Uncertain significance (Feb 12, 2024)
13-36190036-C-T		not specified	Likely benign (Apr 08, 2022)
13-36191833-G-A		SOHLH2-related disorder	Benign (Oct 07, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC169-SOHLH2	protein_coding	protein_coding	ENST00000511166	15	129049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00124	0.998	125731	0	13	125744	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	212	259	0.820	0.0000132	3249
Missense in Polyphen		44	63.531	0.69257		868
Synonymous	0.219	97	99.8	0.972	0.00000563	945
Loss of Function	3.12	10	27.8	0.360	0.00000126	381

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	0.000185	0.000185
European (Non-Finnish)	0.0000445	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000145	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription regulator of both male and female germline differentiation. Suppresses genes involved in spermatogonial stem cells maintenance, and induces genes important for spermatogonial differentiation. Coordinates oocyte differentiation without affecting meiosis I (By similarity). {ECO:0000250|UniProtKB:Q6IUP1, ECO:0000250|UniProtKB:Q9D489}.

Intolerance Scores

• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.55

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.314
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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