Is CCDC180 p.Val55= (c.165G>A) pathogenic?

CCDC180 p.Val55= (c.165G>A) is classified Likely benign in CCDC180 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-01). Very rare (popmax 0.00535%, nfe).

How common is CCDC180 p.Val55= (c.165G>A) in the general population?

CCDC180 p.Val55= (c.165G>A) is very rare (popmax 0.00535%, nfe) (gnomAD).

CCDC180 p.Val55=

c.165G>A · rs374421284 · VCV2659329

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00535%, nfe)

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 1.6	GERP 0.39, phastCons 0.93
Overall
CADD	4.071	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00535% European (non-Finnish) · 63/1,176,878 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00389%

Overall 0.00405% 65/1,606,700 alleles · very rare exomes 60/1,454,598 · genomes 5/152,102 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00535%	18,681
African / African-American	0.00268%	37,261

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: CCDC180
Protein: p.Val55=
Coding: c.165G>A
MANE Select: NM_020893
dbSNP: rs374421284
Type: single nucleotide variant
Location: chr9:97309509 (GRCh38)
Gene constraint: LOEUF 0.821 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.84

Full CCDC180 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC180 p.Val55Leu Uncertain significance ★ ⚠ same residue
CCDC180 p.Ser812Cys Benign ★★ same type
CCDC180 c.-102C>G Uncertain significance ★ ⚠ same type
CCDC180 c.-104C>T Uncertain significance ★ ⚠ same type
CCDC180 c.-107C>G Uncertain significance ★ ⚠ same type
CCDC180 c.-129C>G Uncertain significance ★ ⚠ same type
CCDC180 p.Ala106Thr Uncertain significance ★ ⚠ same type
CCDC180 p.Ala1348Thr 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/ccdc180-p-val55 (accessed [today's date]).

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