Is CCDC32 p.Ser6= (c.18C>T) pathogenic?

CCDC32 p.Ser6= (c.18C>T) is classified Likely benign in CCDC32 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-01). Very rare (popmax 0.00439%, sas).

How common is CCDC32 p.Ser6= (c.18C>T) in the general population?

CCDC32 p.Ser6= (c.18C>T) is very rare (popmax 0.00439%, sas) (gnomAD).

CCDC32 p.Ser6=

c.18C>T · VCV4084024

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00439%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP -3.9, phastCons 0.24
Overall
CADD	3.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00439% South Asian · 4/91,084 alleles

Filtering AF 0.00315% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00279%

Overall 0.00372% 60/1,613,988 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0064%	15,621
South Asiangrpmax	0.00439%	22,771
European (non-Finnish)	0.00407%	24,584
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,604
East Asian	0.00223%	44,902
Admixed American	0.00167%	59,998
African / African-American	0.00133%	74,912

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CCDC32
Protein: p.Ser6=
Coding: c.18C>T
MANE Select: NM_001080792
Type: single nucleotide variant
Location: chr15:40562998 (GRCh38)
Gene constraint: LOEUF 0.76 · pLI 0.19 (gnomAD)
Structure: AlphaFold pLDDT 69.74

Full CCDC32 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC32 c.-13+196A>T Uncertain significance ★ same type
CCDC32 p.Asp45His Uncertain significance ★ ⚠ same type
CCDC32 p.Gly177Arg Uncertain significance ★ ⚠ same type
CCDC32 p.Tyr157Ter Uncertain significance ★ same type
CCDC32 c.402-6939A>C Likely benign ★ same type
CCDC32 c.-13+210T>C Likely benign ★ same type
CCDC32 p.Asp172= Likely benign ★ same type
CCDC32 p.Val76= Likely benign ★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ccdc32-p-ser6 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown