Is CEP19 p.Asp147= (c.441C>T) pathogenic?

CEP19 p.Asp147= (c.441C>T) is classified Likely benign in CEP19 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-30). Very rare (popmax 0.00347%, nfe).

How common is CEP19 p.Asp147= (c.441C>T) in the general population?

CEP19 p.Asp147= (c.441C>T) is very rare (popmax 0.00347%, nfe) (gnomAD).

CEP19 p.Asp147=

c.441C>T · rs375161676 · VCV1963925

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00347%, 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 -0.14	GERP -1.9, phastCons 0.002
Overall
CADD	8.091	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00347% European (non-Finnish) · 41/1,179,900 alleles

Filtering AF 0.00259% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00233%

Overall 0.00267% 43/1,613,360 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00347%	28,778
Remaining individualsnot grpmax-eligible	0.0016%	62,472
South Asian	0.0011%	91,070

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: CEP19
Protein: p.Asp147=
Coding: c.441C>T
MANE Select: NM_032898
dbSNP: rs375161676
Type: single nucleotide variant
Location: chr3:196707602 (GRCh38)
Gene constraint: LOEUF 1.208 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.85

Full CEP19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CEP19 p.Arg32His Uncertain significance ★★ same type
CEP19 p.Arg37Ter Uncertain significance ★★ same type
CEP19 p.Arg95Trp Uncertain significance ★★ same type
CEP19 p.Asn54Ser Uncertain significance ★★ same type
CEP19 p.Gly27Arg Uncertain significance ★★ same type
CEP19 p.Ile33Val Uncertain significance ★★ same type
CEP19 p.Lys111Arg Uncertain significance ★★ same type
CEP19 p.Met1Thr 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/cep19-p-asp147 (accessed [today's date]).

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