Is EIF3F p.Pro7Ser (c.19C>T) pathogenic?

EIF3F p.Pro7Ser (c.19C>T) is classified Likely benign in EIF3F (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-03-05). AlphaMissense: likely benign (0.0608); Rare (popmax 0.16%, sas); Associated with Inborn genetic diseases.

What condition is associated with EIF3F p.Pro7Ser (c.19C>T)?

EIF3F p.Pro7Ser (c.19C>T) is associated with Inborn genetic diseases (ClinVar).

How common is EIF3F p.Pro7Ser (c.19C>T) in the general population?

EIF3F p.Pro7Ser (c.19C>T) is rare (popmax 0.16%, sas) (gnomAD).

What do computational predictors say about EIF3F p.Pro7Ser (c.19C>T)?

AlphaMissense predicts likely benign (score 0.0608) — an in-silico prediction, not a clinical call.

EIF3F p.Pro7Ser

c.19C>T · rs200048982 · VCV2342515

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0608 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.16%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0608	likely benign
REVEL	0.011	strongly benign-leaning
SaProt	LLR -7.67	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 -0.72	GERP -2.6
Regional constraint	o/e 1.40	unconstrained · MANE · 259 bp · p 1.3e-05 · regional, not allelic
Overall
CADD	0.318	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 0.16% South Asian · 145/90,744 alleles

Filtering AF 0.139% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.13%

Overall 0.026% 415/1,595,852 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.299%	335
South Asiangrpmax	0.16%	626
Middle Eastern	0.0993%	1,007
Remaining individualsnot grpmax-eligible	0.0515%	1,943
Finnishnot grpmax-eligible	0.02%	5,000
European (non-Finnish)	0.0106%	9,420
Admixed American	0.00672%	14,888
African / African-American	0.00669%	14,938

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: EIF3F
Protein: p.Pro7Ser
Coding: c.19C>T
MANE Select: NM_003754
dbSNP: rs200048982
Type: single nucleotide variant
Location: chr11:7987371 (GRCh38)
Gene constraint: LOEUF 0.46 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 75.97 · 29 PDB
Residue 7: the 'disordered' region

Full EIF3F gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EIF3F p.Pro7= Likely benign ★★ same residue
EIF3F p.Asp292Glu Uncertain significance ★★ ⚠ same condition
EIF3F c.365-3C>T Uncertain significance ★ same condition
EIF3F p.Ala300Thr Uncertain significance ★ ⚠ same condition
EIF3F p.Ala44Val Uncertain significance ★ ⚠ same condition
EIF3F p.Ala51Gly Uncertain significance ★ ⚠ same condition
EIF3F p.Ala81Gly Uncertain significance ★ ⚠ same condition
EIF3F p.Arg192Gln Uncertain significance ★ ⚠ same condition

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/eif3f-p-pro7ser (accessed [today's date]).

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