Is CCDC152 p.Asn35Ser (c.104A>G) pathogenic?

CCDC152 p.Asn35Ser (c.104A>G) is classified Likely benign in CCDC152 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-02). AlphaMissense: likely benign (0.0558); Ultra-rare (popmax 0.075%, afr).

How common is CCDC152 p.Asn35Ser (c.104A>G) in the general population?

CCDC152 p.Asn35Ser (c.104A>G) is ultra-rare (popmax 0.075%, afr) (gnomAD).

What do computational predictors say about CCDC152 p.Asn35Ser (c.104A>G)?

AlphaMissense predicts likely benign (score 0.0558) — an in-silico prediction, not a clinical call.

CCDC152 p.Asn35Ser

c.104A>G · rs374555478 · VCV2399195

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0558 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.075%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0558	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -6.58	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.18	GERP -1.8, phastCons 0.011
Regional constraint	o/e 0.89	unconstrained · MANE · 41 kb · p 0.053 · regional, not allelic
Overall
CADD	7.531	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 0.075% African / African-American · 54/71,958 alleles

Filtering AF 0.059% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0533%

Overall 0.00537% 81/1,509,694 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.075%	1,333
South Asian	0.0159%	6,308
Remaining individualsnot grpmax-eligible	0.0136%	7,350
Admixed American	0.00407%	24,557
Ashkenazi Jewishnot grpmax-eligible	0.00354%	28,216
European (non-Finnish)	0.00027%	370,810

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: CCDC152
Protein: p.Asn35Ser
Coding: c.104A>G
MANE Select: NM_001134848
dbSNP: rs374555478
Type: single nucleotide variant
Location: chr5:42762459 (GRCh38)
Gene constraint: LOEUF 1.871 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.17

Full CCDC152 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

SELENOP p.Gly230= Benign ★★ same type
CCDC152 p.Ala116Asp Uncertain significance ★ ⚠ same type
CCDC152 p.Ala192Pro Uncertain significance ★ ⚠ same type
CCDC152 p.Ala228Glu Uncertain significance ★ ⚠ same type
CCDC152 p.Arg231His Uncertain significance ★ ⚠ same type
CCDC152 p.Arg253Trp Uncertain significance ★ ⚠ same type
CCDC152 p.Cys66Ser Uncertain significance ★ ⚠ same type
CCDC152 p.Cys8Tyr 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/ccdc152-p-asn35ser (accessed [today's date]).

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