Is CCNDBP1 p.Val155Ala (c.464T>C) pathogenic?

CCNDBP1 p.Val155Ala (c.464T>C) is classified Uncertain significance in CCNDBP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-01). AlphaMissense: ambiguous (0.5539); Ultra-rare (popmax 0.0169%, nfe).

How common is CCNDBP1 p.Val155Ala (c.464T>C) in the general population?

CCNDBP1 p.Val155Ala (c.464T>C) is ultra-rare (popmax 0.0169%, nfe) (gnomAD).

What do computational predictors say about CCNDBP1 p.Val155Ala (c.464T>C)?

AlphaMissense predicts ambiguous (score 0.5539) — an in-silico prediction, not a clinical call.

CCNDBP1 p.Val155Ala

c.464T>C · rs149681338 · VCV3139912

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5539 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0169%, nfe)

Computational evidence

Protein change
AlphaMissense	0.5539	ambiguous
REVEL	0.441	indeterminate
SaProt	LLR -10.27	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 9,339 bp · p 0.77 · regional, not allelic
Overall
CADD	25.0	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

Grpmax group 0.0169% European (non-Finnish) · 200/1,180,026 alleles

Filtering AF 0.015% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0143%

Overall 0.0143% 231/1,614,168 alleles · ultra-rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0676%	1,480
European (non-Finnish)grpmax	0.0169%	5,900
Remaining individualsnot grpmax-eligible	0.0144%	6,945
Admixed American	0.00333%	30,010

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: CCNDBP1
Protein: p.Val155Ala
Coding: c.464T>C
MANE Select: NM_012142
dbSNP: rs149681338
Type: single nucleotide variant
Location: chr15:43190360 (GRCh38)
Gene constraint: LOEUF 1.235 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.38 · 1 PDB
Residue 155: the 'required for interaction with ccnd1' region; the 'interaction with rplp0' region; an α-helix; the 'interaction with tcf3' region

Full CCNDBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCNDBP1 p.Ala121Thr Uncertain significance ★★ ⚠ same type
CCNDBP1 p.Ala158Val Uncertain significance ★ ⚠ same type
CCNDBP1 p.Ala246Ser Uncertain significance ★ ⚠ same type
CCNDBP1 p.Ala246Val Uncertain significance ★ ⚠ same type
CCNDBP1 p.Arg119Gln Uncertain significance ★ ⚠ same type
CCNDBP1 p.Arg22Pro Uncertain significance ★ ⚠ same type
CCNDBP1 p.Arg29Gln Uncertain significance ★ ⚠ same type
CCNDBP1 p.Arg305Gln 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/ccndbp1-p-val155ala (accessed [today's date]).

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