Is CCDC148 p.Gly560= (c.1680A>G) pathogenic?

CCDC148 p.Gly560= (c.1680A>G) is classified Likely benign in CCDC148 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-11-27). Ultra-rare (popmax 0.0421%, amr).

How common is CCDC148 p.Gly560= (c.1680A>G) in the general population?

CCDC148 p.Gly560= (c.1680A>G) is ultra-rare (popmax 0.0421%, amr) (gnomAD).

CCDC148 p.Gly560=

c.1680A>G · rs140240262 · VCV736667

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0421%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.5	GERP -0.65, phastCons 1
Overall
CADD	8.144	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0421% Admixed American · 25/59,418 alleles

Filtering AF 0.0292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.025%

Overall 0.0199% 321/1,609,132 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0421%	2,377
European (non-Finnish)	0.0235%	4,251
Remaining individualsnot grpmax-eligible	0.0193%	5,188
African / African-American	0.00535%	18,704
Finnishnot grpmax-eligible	0.00313%	31,979
South Asian	0.00111%	90,144

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: CCDC148
Protein: p.Gly560=
Coding: c.1680A>G
dbSNP: rs140240262
Type: single nucleotide variant
Location: chr2:158172209 (GRCh38)

Full CCDC148 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/ccdc148-p-gly560 (accessed [today's date]).

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