Is CD1C p.Phe6Leu (c.16T>C) pathogenic?

CD1C p.Phe6Leu (c.16T>C) is classified Likely benign in CD1C (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-17). AlphaMissense: likely benign (0.2325); Absent from gnomAD v4.1.

How common is CD1C p.Phe6Leu (c.16T>C) in the general population?

CD1C p.Phe6Leu (c.16T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD1C p.Phe6Leu (c.16T>C)?

AlphaMissense predicts likely benign (score 0.2325) — an in-silico prediction, not a clinical call.

CD1C p.Phe6Leu

c.16T>C · rs2525996917 · VCV2547350

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2325 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2325	likely benign
REVEL	0.008	strongly benign-leaning
SaProt	LLR -4.49	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.5	GERP -3
Regional constraint	o/e 1.06	unconstrained · MANE · 3,408 bp · p 0.27 · regional, not allelic
Overall
CADD	0.312	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CD1C
Protein: p.Phe6Leu
Coding: c.16T>C
MANE Select: NM_001764 · reported on NM_001765
dbSNP: rs2525996917
Type: single nucleotide variant
Location: chr1:158290080 (GRCh38)

Full CD1C 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/cd1c-p-phe6leu (accessed [today's date]).

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