Is CCDC154 p.Ala5Ser (c.13G>T) pathogenic?

CCDC154 p.Ala5Ser (c.13G>T) is classified Uncertain significance in CCDC154 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-10). Absent from gnomAD v4.1.

How common is CCDC154 p.Ala5Ser (c.13G>T) in the general population?

CCDC154 p.Ala5Ser (c.13G>T) is absent from gnomAD v4.1 (gnomAD).

CCDC154 p.Ala5Ser

c.13G>T · rs1157344478 · VCV3138550

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,299,424)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.037	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP 1.3, phastCons 0.006
Regional constraint	o/e 1.03	unconstrained · MANE · 9,911 bp · p 0.42 · regional, not allelic
Overall
CADD	17.21	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,299,424). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CCDC154
Protein: p.Ala5Ser
Coding: c.13G>T
MANE Select: NM_001143980
dbSNP: rs1157344478
Type: single nucleotide variant
Location: chr16:1444007 (GRCh38)
Gene constraint: LOEUF 1.366 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.92

Full CCDC154 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC154 p.Ala128Val Uncertain significance ★ same type
CCDC154 p.Ala129Gly Uncertain significance ★ same type
CCDC154 p.Ala136Val Uncertain significance ★ same type
CCDC154 p.Ala148Gly Uncertain significance ★ same type
CCDC154 p.Ala14Thr Uncertain significance ★ same type
CCDC154 p.Ala177Val Uncertain significance ★ same type
CCDC154 p.Ala205Val Uncertain significance ★ same type
CCDC154 p.Ala315Val Uncertain significance ★ 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/ccdc154-p-ala5ser (accessed [today's date]).

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