Is CDC14C p.Leu6= (c.16C>T) pathogenic?

CDC14C p.Leu6= (c.16C>T) is classified Likely benign in CDC14C (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-01). Rare (popmax 0.268%, mid).

How common is CDC14C p.Leu6= (c.16C>T) in the general population?

CDC14C p.Leu6= (c.16C>T) is rare (popmax 0.268%, mid) (gnomAD).

CDC14C p.Leu6=

c.16C>T · rs191352971 · VCV2657496

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.268%, mid)

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 0.46	GERP -1.7, phastCons 1
Overall
CADD	0.944	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.268% Middle Eastern · 14/5,224 alleles

Filtering AF 0.182% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.171%

Overall 0.13% 1,518/1,170,024 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.29%	345
Middle Easterngrpmax	0.268%	373
Admixed American	0.212%	471
Remaining individualsnot grpmax-eligible	0.171%	583
European (non-Finnish)	0.152%	656
African / African-American	0.0227%	4,406
South Asian	0.0195%	5,129
Finnishnot grpmax-eligible	0.00787%	12,712

Ashkenazi Jewish 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: CDC14C
Protein: p.Leu6=
Coding: c.16C>T
MANE Select: NM_152627
dbSNP: rs191352971
Type: single nucleotide variant
Location: chr7:48924688 (GRCh38)
Gene constraint: LOEUF 1.434 · pLI 0.07 (gnomAD)
Structure: AlphaFold pLDDT 85.91

Full CDC14C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/cdc14c-p-leu6 (accessed [today's date]).

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